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The Lesser Antillean island chain in the eastern Caribbean formerly supported a diverse rodent fauna including multiple endemic genera of oryzomyine rice rats. The Caribbean rice rats are now all extinct, with most island populations known only from Holocene palaeontological and zooarchaeological material and with many remaining taxonomically undescribed. Rice rat material is reported from several pre-Columbian Ceramic Age (late Holocene) archaeological sites on the Grenada Bank, including sites on Grenada and Carriacou, but the taxonomic identity and diversity of the Grenada Bank rice rats has remained uncertain. We provide a morphology-based description of rice rats from Grenada and Carriacou, and analyze their phylogenetic and biogeographical affinities to other Caribbean and mainland Neotropical oryzomyines. We recognize two taxa from the Grenada Bank: we describe the new species Megalomys camerhogne from Pearls (Grenada), representing the largest-bodied member of the extinct endemic Caribbean genus Megalomys, and we refer smaller-bodied oryzomyine material from Pearls and Sabazan (Carriacou) to the widespread extant Neotropical species Zygodontomys brevicauda. Body size variation within Megalomys correlates with island bank area and might thus reflect historical rather than modern biogeography. Zygodontomys specimens from the Grenada Bank fall within the upper end of size variation in extant populations and may constitute an example of 'island gigantism', but it is possible that occurrence of this widespread species on the Grenada Bank might reflect prehistoric human-mediated translocation. We predict further endemic Caribbean rice rat taxa remain to be discovered, including a possible species of Megalomys on the neighbouring island of St. Vincent.

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Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have experienced the globally highest level of human-caused postglacial mammalian extinctions, and included all extinct and extant Holocene island populations of non-volant species (219 survivals or extinctions across 118 islands). Extinction selectivity shows a statistically detectable and complex body mass effect, with survival probability decreasing for both mass extremes, indicating that intermediate-sized species have been more resilient. A strong interaction between mass and age of first human arrival provides quantitative evidence of larger mammals going extinct on the earliest islands colonized, revealing an extinction filter caused by past human activities. Survival probability increases on islands with lower mean elevation (mostly small cays acting as offshore refugia) and decreases with more frequent hurricanes, highlighting the risk of extreme weather events and rising sea levels to surviving species on low-lying cays. These findings demonstrate the interplay between intrinsic biology, regional ecology and specific local threats, providing insights for understanding drivers of biodiversity loss across island systems and fragmented habitats worldwide.

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The International Union for Conservation of Nature's Red List of Threatened Species (RLS) is the key global tool for objective, repeatable assessment of species' extinction risk status, and plays an essential role in tracking biodiversity loss and guiding conservation action. Satellite remote sensing (SRS) data sets on global ecosystem distributions and functioning show exciting potential for informing range-based RLS assessment, but their incorporation has been restricted by low temporal resolution and coverage of data sets, lack of incorporation of degradation-driven habitat loss, and noninclusion of assumptions related to identification of changing habitat distributions for taxa with varying habitat dependency and ecologies. For poorly known mangrove-associated Cuban hutias (Mesocapromys spp.), we tested the impact of possible assumptions regarding these issues on range-based RLS assessment outcomes. Specifically, we used annual (1985-2018) Landsat data and land-cover classification and habitat degradation analyses across different internal time series slices to simulate range-based RLS assessments for our case study taxa to explore potential assessment uncertainty arising from temporal SRS data set coverage, incorporating proxies of (change in) habitat quality, and assumptions on spatial scaling of habitat extent for RLS parameter generation. We found extensive variation in simulated species-specific range-based RLS assessments, and this variation was mostly associated with the time series over which parameters were estimated. However, results of some species-specific assessments differed by up to 3 categories (near threatened to critically endangered) within the same time series, due to the effects of incorporating habitat quality and the spatial scaling used in RLS parameter estimation. Our results showed that a one-size-fits-all approach to incorporating SRS information in RLS assessment is inappropriate, and we urge caution in conducting range-based assessments with SRS for species for which habitat dependence on specific ecosystem types is incompletely understood. We propose novel revisions to parameter spatial scaling guidelines to improve integration of existing time series data on ecosystem change into the RLS assessment process.

La Lista Roja de Especies Amenazadas (LREA) de la Unión Internacional para la Conservación de la Naturaleza es la herramienta mundial más importante para la evaluación objetiva y repetible del estado de riesgo de extinción de una especie y juega un papel esencial en el seguimiento de la pérdida de la biodiversidad y en la orientación de las acciones de conservación. Los conjuntos de datos obtenidos por telemetría satelital (SRS) sobre la distribución y funcionamiento de los ecosistemas globales tienen un potencial emocionante para informar las evaluaciones de la LREA basadas en la extensión de la distribución de la especie, pero su incorporación dentro de los estudios ha estado restringida por la baja resolución temporal y la poca cobertura de los conjuntos de datos, la falta de inclusión de la pérdida de hábitat causada por la degradación y la nula inclusión de las suposiciones relacionadas con la identificación del cambio de hábitat de distribución para los taxones con una ecología y una dependencia por el hábitat variantes. Analizamos el impacto de las posibles suposiciones con respecto a los tres temas anteriores sobre los resultados de la evaluación de la LREA basada en la distribución de la jutía cubana (Mesocapromys spp.), una especie poco conocida y asociada con manglares. Específicamente, usamos los datos anuales (1985-2018) de Landsat y de la clasificación del uso de suelo y los análisis de degradación del hábitat en diferentes porciones de series temporales internas para simular las evaluaciones de la LREA basadas en la extensión para nuestro taxón de estudio y así explorar la incertidumbre potencial de la evaluación que surge de la cobertura del conjunto de datos SRS temporales. También incorporamos sustitutos de (cambio en) la calidad del hábitat y suposiciones sobre la escala espacial de la extensión del hábitat para la generación de parámetros de la LREA. Encontramos una variación extensa en las evaluaciones simuladas de la LREA específicas de especie y basadas en la extensión. Esta variación estuvo principalmente asociada con la serie temporal sobre la cual se estimaron los parámetros. Sin embargo, los resultados de algunas evaluaciones específicas de especie difirieron hasta en tres categorías (de casi amenazada hasta en peligro crítico) dentro de la misma serie temporal debido a los efectos de la incorporación de la calidad del hábitat y la escala espacial usadas en la estimación de parámetros de la LREA. Nuestros resultados muestran que un enfoque genérico para incorporar la información de SRS en la evaluación de la LREA es inapropiado e instamos precaución al realizar evaluaciones basadas en la extensión con datos SRS para especies cuya dependencia de hábitat por tipos específicos de ecosistemas no está entendida por completo. Proponemos que existan revisiones novedosas de las pautas para los parámetros de las escalas espaciales y así mejorar la integración de los datos existentes de series temporales sobre el cambio en el ecosistema dentro de los procesos de evaluación de RLS. Identificación de las Posibilidades y las Dificultades para la Realización de Evaluaciones de la Lista Roja de la UICN a partir de Información de Hábitat Detectada Remotamente con base en la Información sobre Mamíferos Cubanos Poco Conocidos.

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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.

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BACKGROUND: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island. RESULTS: Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs. CONCLUSIONS: Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.

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The Hispaniolan solenodon, Solenodon paradoxus, and Hispaniolan hutia, Plagiodontia aedium, are the Dominican Republic's only surviving endemic non-volant land mammals, and are high priorities for conservation. The country has an extensive protected area (PA) network designed to maintain habitats and benefit biodiversity, but which faces significant anthropogenic threats likely to detrimentally impact both species. We examined how differences in habitats, forest structure, topography, and human activity influence presence of solenodons and hutias across the Dominican Republic. Systematic surveys of seven PAs were undertaken to record indirect signs, with presence-absence data analyzed using a multi-model inference approach incorporating ecological variables from both field and GIS data. Solenodons were detected relatively frequently, whereas detections of hutias were uncommon. Lower elevations, increased surrounding tree cover, canopy closure, and reduced levels of low vegetation are all associated with increased probability of detecting solenodons, whereas agriculture and mangrove represent poor-quality habitat. Increased canopy closure, tree basal area (indicating older-growth forest), and increased rock substrate (providing more den sites) are associated with increased probability of detecting hutias. Our findings indicated that human activities within PAs are likely to negatively affect both species, and conservation activities should focus on preventing encroachment and conversion of forest to agriculture to maintain high-quality forest habitats. El solenodonte de la Hispaniola, Solenodon paradoxus, y la hutia de la Hispaniola, Plagiodontia aedium, son los únicos mamíferos endémicos terrestres no voladores que sobreviven en la República Dominicana, su conservación es de alta prioridad. El país tiene una extensa red de áreas protegidas (AP) diseñada para mantener hábitats y beneficiar la biodiversidad, pero se enfrenta a amenazas antropogénicas. Sin embargo, no existen datos cuantitativos para evaluar las presiones antropogénicas que amenazan a los solenodontes y las hutias. Examinamos cómo las diferencias en los hábitats, la estructura del bosque, la topografía y la actividad humana influyen la presencia de solenodontes y hutias en toda la República Dominicana. Se realizaron encuestas sistemáticas de siete AP para registrar los signos indirectos de ambas especies, los datos de presencia/ausencia fueron analizados mediante inferencia multimodelo que incorpora variables ecológicas de los datos de campo y Sistema de Información Geográfica. Los Solenodontes se detectaron relativamente frecuentemente, mientras que las detecciones de hutias fueron menos comunes. Las elevaciones más bajas, el aumento de la cubierta arbórea circundante, el cierre del dosel y los niveles reducidos de vegetación baja se asocian con una mayor probabilidad de detectar solenodones. Mientras que la agricultura y los manglares representan un hábitat de mala calidad para el solenodonte. Aumento del cierre del dosel, área basal del árbol (que indica un bosque más antiguo) y un sustrato con mayor proporcion de roca (que proporciona más sitios para madrigueras) se asocian con una mayor probabilidad de detectar hutias. Nuestros hallazgos indican que las actividades humanas dentro de las AP pueden afectar negativamente a ambas especies. Las actividades de conservación deberían enfocarse en mantener hábitats forestales de alta calidad por medio de prevenir la invasión y la conversión de los bosques a agricultura.

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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.

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Insular giant tortoise diversity has been depleted by Late Quaternary extinctions, but the taxonomic status of many extinct populations remains poorly understood due to limited available fossil or subfossil material, hindering our ability to reconstruct Quaternary island biotas and environments. Giant tortoises are absent from current-day insular Caribbean ecosystems, but tortoise remains from Quaternary deposits indicate the former widespread occurrence of these animals across the northern Caribbean. We report new Quaternary giant tortoise material from several cave sites in Pedernales Province, southern Dominican Republic, Hispaniola, representing at least seven individuals, which we describe as Chelonoidis marcanoi sp. nov. Although giant tortoise material was first reported from the Quaternary record of Hispaniola almost 35 years ago, tortoises are absent from most Quaternary deposits on the island, which has been studied extensively over the past century. The surprising abundance of giant tortoise remains in both vertical and horizontal caves in Hispaniola's semi-arid ecoregion may indicate that this species was adapted to open dry habitats and became restricted to a habitat refugium in southeastern Hispaniola following climatic-driven environmental change at the Pleistocene-Holocene boundary. Hispaniola's dry forest ecosystem may therefore have been shaped by giant tortoises for much of its evolutionary history.

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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.

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Continued uncertainty persists over the taxonomic status of many threatened Caribbean mammal populations. Recent molecular analysis has identified three genetically isolated allopatric hutia populations on Hispaniola that diverged during the Middle Pleistocene, with observed levels of sequence divergence interpreted as representing subspecies-level differentiation through comparison with genetic data for other capromyids. Subsequent analysis of existing museum specimens has demonstrated biogeographically congruent morphometric differentiation for two of these three populations, Plagiodontia aedium aedium (southwestern population) and P. aedium hylaeum (northern population). We report the first craniodental material for the southeastern Hispaniolan hutia population, and demonstrate that this population can also be differentiated using quantitative morphometric analysis from other Hispaniolan hutia subspecies. The holotype skull of P. aedium aedium, of unknown geographic provenance within Hispaniola, clusters morphometrically with the southwestern population. The southeastern Hispaniolan subspecies is described as Plagiodontia aedium bondi subsp. nov., and is assessed as Endangered under Criterion B1a,biii,v on the IUCN Red List.

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No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.

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Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the island's endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the island's biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the island's geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniola's geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).

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A new extinct Late Quaternary platyrrhine from Haiti, Insulacebus toussaintiana, is described here from the most complete Caribbean subfossil primate dentition yet recorded, demonstrating the likely coexistence of two primate species on Hispaniola. Like other Caribbean platyrrhines, I. toussaintiana exhibits primitive features resembling early Middle Miocene Patagonian fossils, reflecting an early derivation before the Amazonian community of modern New World anthropoids was configured. This, in combination with the young age of the fossils, provides a unique opportunity to examine a different parallel radiation of platyrrhines that survived into modern times, but is only distantly related to extant mainland forms. Their ecological novelty is indicated by their unique dental proportions, and by their relatively large estimated body weights, possibly an island effect, which places the group in a size class not exploited by mainland South American monkeys. Several features tie the new species to the extinct Jamaican monkey Xenothrix mcgregori, perhaps providing additional evidence for an inter-Antillean clade.

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