Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

Pliocene sigmodontine rodents (Mammalia: Cricetidae) in northernmost South America: test of biogeographic hypotheses and revised evolutionary scenarios

We document the first occurrence of Sigmodontinae (Mammalia, Rodentia, Cricetidae) from the Pliocene of northern South America, from the San Gregorio Formation of northwestern Venezuela. The recovered isolated molars are identified as Oligoryzomys sp. and Zygodontomys sp., two currently widespread sigmodontines in South America. These records constitute the oldest representatives of these genera, potentially new species, and the first Pliocene occurrence for Oryzomyini and the whole subfamily outside Argentina. Hypotheses on the historical biogeography of sigmodontines have been constructed almost exclusively using genetic data and the fossils we report provide a new kind of evidence. The occurrence of Oligoryzomys sp. and Zygodontomys sp. in Venezuela provides novel information for the diversification models suggested for Oligoryzomys, by supporting a potential eastern corridor of open environments from northern to southern South America. The presence of sigmodontines from the locality home of the new reports, Norte Casa Chiguaje, is consistent with the palaeoenvironmental conditions originally proposed for it based on mammals and botanical records, being characterized as mixed open grassland/forest areas surrounding permanent freshwater systems. The new sigmodontine evidence is used to discuss the putative scenarios of the ancient evolution of the subfamily in South America, favouring a model in which open areas (savannahs) to the east of the Andes played crucial role aiding or obstructing Late Miocene-Pliocene sigmodontine dispersion southwards.

Hidden diversity of the genus Trinomys (Rodentia: Echimyidae): phylogenetic and populational structure analyses uncover putative new lineages

Trinomys, one of the most species-rich spiny rat genera in Brazil, is widely distributed in Caatinga, Cerrado and Atlantic Forest biomes, and currently includes ten recognized species, three of which are polytypic. Although some studies employing molecular data have been conducted to better characterize phylogenetic relationships among species, 19 nominal taxa have been suggested, implying considerable incongruence regarding species boundaries. We addressed this incongruence by intensively sampling all species across the geographic distribution of the genus. In addition to publicly available data, we generated 182 mt-Cytb gene sequences, and employed phylogenetic and computational species delimitation methods to obtain a clearer picture of the genus diversity. Moreover, we evaluated populational diversity within each accepted species, considering their geographical distribution and a timescale for the evolution of the genus. Beyond confirming the general patterns described for the evolution of the group, this new analysis suggests that Trinomys is comprised of at least 16 evolutionary lineages, 13 of them recognized as species or subspecies, and three never before characterized. This study highlights the importance of increased sample sizes and computational species delimitation methods in uncovering hidden diversity in Trinomys.

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.

A comparative analysis of extraction protocol performance on degraded mammalian museum specimens

The extraction of nucleic acids is one of the most routine procedures used in molecular biology laboratories, yet kit performance may influence the downstream processing of samples, particularly for samples which are degraded, and in low concentrations. Here we tested several commercial kits for specific use on commonly sampled mammalian museum specimens to evaluate the yield, size distribution, and endogenous content. Samples were weighed and had approximately equal input material for each extraction. These sample types are typical of natural history repositories ranged from 53 to 130 years old. The tested protocols spanned spin-column based extractions, magnetic bead purification, phenol/chloroform isolation, and specific modifications for ancient DNA. Diverse types of mammalian specimens were tested including adherent osteological material, bone and teeth, skin, and baleen. The concentration of DNA was quantified via fluorometry, and the size distributions of extracts visualized on an Agilent TapeStation. Overall, when DNA isolation was successful, all methods had quantifiable concentrations, albeit with variation across extracts. The length distributions varied based on the extraction protocol used. Shotgun sequencing was performed to evaluate if the extraction methods influenced the amount of endogenous versus exogenous content. The DNA content was similar across extraction methods indicating no obvious biases for DNA derived from different sources. Qiagen kits and phenol/chloroform isolation outperformed the Zymo magnetic bead isolations in these types of samples. Statistical analyses revealed that extraction method only explained 5% of the observed variation, and that specimen age explained variation (29%) more effectively.

Poor hDNA-Derived NGS Data May Provide Sufficient Phylogenetic Information of Potentially Extinct Taxa

Museum material is an important source of metadata for past and recent biological events. With current sequencing technologies, it is possible to obtain historical DNA (hDNA) from older material and/or endangered species to answer taxonomic, systematic, and biogeographical questions. However, hDNA from museum collections is often highly degraded, making it difficult to assess relationships at or above the species level. We therefore studied two probably extinct gastropod species of the genus Laevicaspia, which were collected ∼140 years ago in the Caspian Sea, to map “standard” mitochondrial and nuclear markers and assess both the sequencing depth and the proportion of ambiguous sites as an indicator for the phylogenetic quality of the NGS data. Our study resulted in the first phylogenetically informative mitochondrial and nuclear markers for L. caspia. Assessment of both sequencing depth (mean coverage) and proportion of ambiguous sites suggests that our assembled consensus sequences are reliable for this species. In contrast, no informative gastropod-specific DNA was obtained for L. conus, likely due to a high degree of tissue digestion and contamination with non-gastropod DNA. Nevertheless, our results show that hDNA may in principle yield high-quality sequences for species-level phylogenetic analyses, which underlines the importance of museum collections as valuable archives of the biological past.

Single-Island Endemism despite Repeated Dispersal in Caribbean Micrathena (Araneae: Araneidae): An Updated Phylogeographic Analysis

Island biogeographers have long sought to elucidate the mechanisms behind biodiversity genesis. The Caribbean presents a unique stage on which to analyze the diversification process, due to the geologic diversity among the islands and the rich biotic diversity with high levels of island endemism. The colonization of such islands may reflect geologic heterogeneity through vicariant processes and/ or involve long-distance overwater dispersal. Here, we explore the phylogeography of the Caribbean and proximal mainland spiny orbweavers (Micrathena, Araneae), an American spider lineage that is the most diverse in the tropics and is found throughout the Caribbean. We specifically test whether the vicariant colonization via the contested GAARlandia landbridge (putatively emergent 33–35 mya), long-distance dispersal (LDD), or both processes best explain the modern Micrathena distribution. We reconstruct the phylogeny and test biogeographic hypotheses using a ‘target gene approach’ with three molecular markers (CO1, ITS-2, and 16S rRNA). Phylogenetic analyses support the monophyly of the genus but reject the monophyly of Caribbean Micrathena. Biogeographical analyses support five independent colonizations of the region via multiple overwater dispersal events, primarily from North/Central America, although the genus is South American in origin. There is no evidence for dispersal to the Greater Antilles during the timespan of GAARlandia. Our phylogeny implies greater species richness in the Caribbean than previously known, with two putative species of M. forcipata that are each single-island endemics, as well as deep divergences between the Mexican and Floridian M. sagittata. Micrathena is an unusual lineage among arachnids, having colonized the Caribbean multiple times via overwater dispersal after the submergence of GAARlandia. On the other hand, single-island endemism and undiscovered diversity are nearly universal among all but the most dispersal-prone arachnid groups in the Caribbean.

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

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.

Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini)

Understanding how and why some groups have become more species-rich than others, and how past biogeography may have shaped their current distribution, are questions that evolutionary biologists have long attempted to answer. We investigated diversification patterns and historical biogeography of a hyperdiverse lineage of Lepidoptera, the geometrid moths, by studying its most species-rich tribe Boarmiini, which comprises ca. 200 genera and ca. known 3000 species. We inferred the evolutionary relationships of Boarmiini based on a dataset of 346 taxa, with up to eight genetic markers under a maximum likelihood approach. The monophyly of Boarmiini is strongly supported. However, the phylogenetic position of many taxa does not agree with current taxonomy, although the monophyly of most major genera within the tribe is supported after minor adjustments. Three genera are synonymized, one new combination is proposed, and four species are placed in incertae sedis within Boarmiini. Our results support the idea of a rapid initial diversification of Boarmiini, which also implies that no major taxonomic subdivisions of the group can currently be proposed. A time-calibrated tree and biogeographical analyses suggest that boarmiines appeared in Laurasia ca. 52 Mya, followed by dispersal events throughout the Australasian, African and Neotropical regions. Most of the transcontinental dispersal events occurred in the Eocene, a period of intense geological activity and rapid climate change. Diversification analyses showed a relatively constant diversification rate for all Boarmiini, except in one clade containing the species-rich genus Cleora. The present work represents a substantial contribution towards understanding the evolutionary origin of Boarmiini moths. Our results, inevitably biased by taxon sampling, highlight the difficulties with working on species-rich groups that have not received much attention outside of Europe. Specifically, poor knowledge of the natural history of geometrids (particularly in tropical clades) limits our ability to identify key innovations underlying the diversification of boarmiines.

Historical, allometric and ecological effects on the shape of the lumbar vertebrae of spiny rats (Rodentia: Echimyidae)

In mammals, the lumbar vertebrae are important for sustaining the trunk, for allowing the trunk to flex and extend, and, during locomotion, for transferring forces from the sacroiliac region to the anterior region of the body. The Echimyidae is a group that comprises spiny rats, the coypu and hutias. It is the caviomorph rodent family with the greatest ecological diversity and species richness, as well as having a wide variation in body mass. Thus, echimyid rodents provide a promising model for understanding how phylogenetic, allometric and ecological factors associated with locomotion affect the evolution of the post-cranial skeleton. To assess the effect of these three factors on the morphology of the lumbar vertebrae, the penultimate lumbar vertebra of 26 echimyid species was photographed under five views and submitted to phylogenetically informed comparative analysis using 2D geometric morphometrics. Vertebral shape variation showed a low correlation with body mass and vertebral size, and a low to moderate phylogenetic signal. Remarkably, locomotory habit had a strong influence on lumbar morphology, particularly when analysed in lateral view. Our results indicate that the echimyid penultimate lumbar vertebra is potentially useful for future ecomorphological studies on living and fossil small mammals.

Biogeography of the West Indies: A complex scenario for species radiations in terrestrial and aquatic habitats

Studies of the biogeography of the West Indies are numerous but not all taxonomic groups have received the same attention. Many of the contributions to this field have historically focused on terrestrial vertebrates from a perspective closely linked to the classical theory of island biogeography. However, some recent works have questioned whether some of the assumptions of this theory are too simplistic. In this review, we compiled information about the West Indies biogeography based on an extensive and rigorous literature search. While we offer some background of the main hypotheses that explain the origin of the Caribbean biota, our main purpose here is to highlight divergent diversification patterns observed in terrestrial versus aquatic groups of the West Indian biota and also to shed light on the unbalanced number of studies covering the biogeography of these groups of organisms. We use an objective method to compile existing information in the field and produce a rigorous literature review. Our results show that most of the relevant literature in the field is related to the study of terrestrial organisms (mainly vertebrates) and only a small portion covers aquatic groups. Specifically, livebearing fishes show interesting deviations from the species-area relationship predicted by classical island biogeography theory. We found that species richness on the Greater Antilles is positively correlated with island size but also with the presence of elevations showing that not only island area but also mountainous relief may be an important factor determining the number of freshwater species in the Greater Antilles. Our findings shed light on mechanisms that may differently drive speciation in aquatic versus terrestrial environments suggesting that ecological opportunity could outweigh the importance of island size in speciation. Investigations into freshwater fishes of the West Indies offer a promising avenue for understanding origins and subsequent diversification of the Caribbean biota.

Effects of size, phylogeny and locomotor habits on the pelvic and femoral morphology of South American spiny rats (Rodentia: Echimyidae)

The rodent family Echimyidae (spiny rats, hutias and coypu) is notable for its high phylogenetic and ecological diversity, encompassing ~100 living species with body mass ranging from 70 to 4500 g, including arboreal, epigean (non-arboreal or scansorial), fossorial and semi-aquatic taxa. In view of this diversity, it was hypothesized that echimyid morphological variation in the pelvis and femur should reflect: (1) allometric association with body mass; (2) morphofunctional specializations for the different locomotor habits; and (3) phylogenetic history. To test these propositions, we examined 30 echimyid species, in addition to eight species of two other octodontoid families, Abrocomidae and Octodontidae. Pelvic and femoral variation was assessed with linear morphometry, using bivariate and multivariate statistical methods, part of which was phylogenetically informed. Approximately 80% of the total variation among echimyids was explained by body mass, and some univariate measurements were found potentially to be effective as body mass estimators after simple allometric procedures, notably in the pelvis. Even considering the significant phylogenetic signal, variation in shape was largely structured by locomotor habits, mainly in the pelvis, suggesting that the echimyid hindlimb diversification was driven, in part, by selective pressures related to locomotor habits. Finally, echimyid femoral disparity was considerably greater than in other octodontoids, contrasting with their relatively modest cranial variation. Thus, this study suggests that hindlimb diversity constitutes a key factor for the exceptional echimyid ecological and phyletic diversification.

Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews)

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens

OBJECTIVES

Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens.

METHODS

We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia.

RESULTS

We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra.

CONCLUSIONS

Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.

The earliest record of Caribbean frogs: a fossil coquí from Puerto Rico

The nearly 200 species of direct-developing frogs in the genus Eleutherodactylus (the Caribbean landfrogs, which include the coquís) comprise an important lineage for understanding the evolution and historical biogeography of the Caribbean. Time-calibrated molecular phylogenies provide indirect evidence for the processes that shaped the modern anuran fauna, but there is little direct evidence from the fossil record of Caribbean frogs about their distributions in the past. We report a distal humerus of a frog from the Oligocene (approx. 29 Ma) of Puerto Rico that represents the earliest known fossil frog from any Caribbean island. Based on its prominent rounded distal humeral head, distally projecting entepicondyle, and reduced ectepicondyle, we refer it to the genus Eleutherodactylus. This fossil provides additional support for an early arrival of some groups of terrestrial vertebrates to the Greater Antilles and corroborates previous estimates based on molecular phylogenies suggesting that this diverse Caribbean lineage was present in the islands by the mid-Cenozoic.

Early Oligocene chinchilloid caviomorphs from Puerto Rico and the initial rodent colonization of the West Indies

By their past and present diversity, rodents are among the richest components of Caribbean land mammals. Many of these became extinct recently. Causes of their extirpation, their phylogenetic affinities, the timing of their arrival in the West Indies and their biogeographic history are all ongoing debated issues. Here, we report the discovery of dental remains from Lower Oligocene deposits (ca 29.5 Ma) of Puerto Rico. Their morphology attests to the presence of two distinct species of chinchilloid caviomorphs, closely related to dinomyids in a phylogenetic analysis, and thus of undisputable South American origin. These fossils represent the earliest Caribbean rodents known thus far. They could extend back to 30 Ma the lineages of some recently extinct Caribbean giant rodents (Elasmodontomys and Amblyrhiza), which are also retrieved here as chinchilloids. This new find has substantial biogeographic implications because it demonstrates an early dispersal of land mammals from South America to the West Indies, perhaps via the emergence of the Aves Ridge that occurred ca 35-33 Ma (GAARlandia hypothesis). Considering both this new palaeontological evidence and recent molecular divergence estimates, the natural colonization of the West Indies by rodents probably occurred through multiple and time-staggered dispersal events (chinchilloids, then echimyid octodontoids (spiny rats/hutias), caviids and lastly oryzomyin muroids (rice rats)).

Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia

Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.

The zooarchaeology and isotopic ecology of the Bahamian hutia (Geocapromys ingrahami): Evidence for pre-Columbian anthropogenic management

Bahamian hutias (Geocapromys ingrahami) are the only endemic terrestrial mammal in The Bahamas and are currently classified as a vulnerable species. Drawing on zooarchaeological and new geochemical datasets, this study investigates human management of Bahamian hutias as cultural practice at indigenous Lucayan settlements in The Bahamas and the Turks & Caicos Islands. In order to determine how hutia diet and distribution together were influenced by Lucayan groups we conducted isotopic analysis on native hutia bone and tooth enamel recovered at the Major’s Landing site on Crooked Island in The Bahamas and introduced hutias from the Palmetto Junction site on Providenciales in the Turks & Caicos Islands. Results indicate that some hutias consumed ¹³C-enriched foods that were either provisioned or available for opportunistic consumption. Strontium isotope ratios for hutia tooth enamel show a narrow range consistent with local origin for all of the archaeological specimens. In contrast, analysis of strontium isotopes in modern Bahamian hutia teeth from animals relocated to Florida from The Bahamas demonstrates that these animals rapidly lost their Bahamian signature and adopted a Florida signature. Therefore, strontium should be used cautiously for determining hutia provenance, particularly for individuals that were translocated between islands. Overall, our findings suggest that ancient human presence did not always result in hutia vulnerability and that the impact to hutia populations was variable across pre-Columbian indigenous settlements.

Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths

Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.

Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily

Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias - formerly placed in the Capromyidae family - as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.

Biogeography of the Caribbean Cyrtognatha spiders

Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genus Cyrtognatha (Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test if Cyrtognatha biogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampled Cyrtognatha individuals, using models with and without a founder event parameter. Our results suggest a radiation of Caribbean Cyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola, Cyrtognatha subsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event.

The role of Pleistocene climate change in the genetic variability, distribution and demography of Proechimys cuvieri and P. guyannensis (Rodentia: Echimyidae) in northeastern Amazonia

The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.

Evolutionary Patterns and Processes: Lessons from Ancient DNA

Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.

The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species

The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.

Anthropogenic Extinction Dominates Holocene Declines of West Indian Mammals

The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.

A Cretaceous-aged Palaeotropical dispersal established an endemic lineage of Caribbean praying mantises

Recent phylogenetic advances have uncovered remarkable biogeographic histories that have challenged traditional concepts of dispersal, vicariance and diversification in the Greater Antilles. Much of this focus has centred on vertebrate lineages despite the high diversity and endemism of terrestrial arthropods, which account for 2.5 times the generic endemism of all Antillean plants and non-marine vertebrates combined. In this study, we focus on three Antillean endemic praying mantis genera, Callimantis, Epaphrodita and Gonatista, to determine their phylogenetic placement and geographical origins. Each genus is enigmatic in their relation to other praying mantises due to their morphological affinities with both Neotropical and Old World groups. We recovered the three genera as a monophyletic lineage among Old World groups, which was supported by molecular and morphological evidence. With a divergence at approximately 107 Ma, the lineage originated during the break-up of Gondwana. Ancestral range reconstruction indicates the lineage dispersed from an African + Indomalayan range to the Greater Antilles, with a subsequent extinction in the Old World. The profound ecomorphic convergence with non-Caribbean groups obscured recognition of natural relationships within the same geographical distribution. To the best of our knowledge, the lineage is one of the oldest endemic animal groups in the Greater Antilles and their morphological diversity and restricted distribution mark them as a critical taxon to conserve.

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.

Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family

The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ∼750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.

Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon

The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised.

Late Pleistocene echimyid rodents (Rodentia, Hystricognathi) from northern Brazil

ABSTRACT Echimyidae (spiny rats, tree rats and the coypu) is the most diverse family of extant South American hystricognath rodents (caviomorphs). Today, they live in tropical forests (Amazonian, coastal and Andean forests), occasionally in more open xeric habitats in the Cerrado and Caatinga of northern South America, and open areas across the southern portion of the continent (Myocastor). The Quaternary fossil record of this family remains poorly studied. Here, we describe the fossil echimyids found in karst deposits from southern Tocantins, northern Brazil. The analyzed specimens are assigned to Thrichomys sp., Makalata cf. didelphoides and Proechimys sp. This is the first time that a fossil of Makalata is reported. The Pleistocene record of echimyids from this area is represented by fragmentary remains, which hinders their determination at specific levels. The data reported here contributes to the understanding of the ancient diversity of rodents of this region, evidenced until now in other groups, such as the artiodactyls, cingulates, carnivores, marsupials, and squamate reptiles.

Geological Changes of the Americas and their Influence on the Diversification of the Neotropical Kissing Bugs (Hemiptera: Reduviidae: Triatominae)

BACKGROUND

The family Reduviidae (Hemiptera: Heteroptera), or assassin bugs, is among the most diverse families of the true bugs, with more than 6,000 species. The subfamily Triatominae (kissing bugs) is noteworthy not simply because it is the only subfamily of the Reduviidae whose members feed on vertebrate blood but particularly because all 147 known members of the subfamily are potential Chagas disease vectors. Due to the epidemiological relevance of these species and the lack of an efficient treatment and vaccine for Chagas disease, it is more common to find evolutionary studies focusing on the most relevant vectors than it is to find studies aiming to understand the evolution of the group as a whole. We present the first comprehensive phylogenetic study aiming to understand the events that led to the diversification of the Triatominae.

METHODOLOGY/PRINCIPAL FINDINGS

We gathered the most diverse samples of Reduviidae and Triatominae (a total of 229 Reduviidae samples, including 70 Triatominae species) and reconstructed a robust dated phylogeny with several fossil (Reduviidae and Triatominae) calibrations. Based on this information, the possible role of geological events in several of the major cladogenetic events within Triatominae was tested for the first time. We were able to not only correlate the geological changes in the Neotropics with Triatominae evolution but also add to an old discussion: Triatominae monophyly vs. paraphyly.

CONCLUSIONS/SIGNIFICANCE

We found that most of the diversification events observed within the Rhodniini and Triatomini tribes are closely linked to the climatic and geological changes caused by the Andean uplift in South America and that variations in sea levels in North America also played a role in the diversification of the species of Triatoma in that region.

Spintharus flavidus in the Caribbean-a 30 million year biogeographical history and radiation of a 'widespread species'

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species,’ presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others are single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.

Pros and cons of methylation-based enrichment methods for ancient DNA

The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

Reconstructing ancient genomes and epigenomes

Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.