Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives

Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000–944 000), points toward an island colonization during the Günz–Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.     

Unexpected evolutionary diversity in a recently extinct Caribbean mammal radiation

Identifying general patterns of colonization and radiation in island faunas is often hindered by past human-caused extinctions. The insular Caribbean is one of the only complex oceanic-type island systems colonized by land mammals, but has witnessed the globally highest level of mammalian extinction during the Holocene. Using ancient DNA analysis, we reconstruct the evolutionary history of one of the Caribbean''s now-extinct major mammal groups, the insular radiation of oryzomyine rice rats. Despite the significant problems of recovering DNA from prehistoric tropical archaeological material, it was possible to identify two discrete Late Miocene colonizations of the main Lesser Antillean island chain from mainland South America by oryzomyine lineages that were only distantly related. A high level of phylogenetic diversification was observed within oryzomyines across the Lesser Antilles, even between allopatric populations on the same island bank. The timing of oryzomyine colonization is closely similar to the age of several other Caribbean vertebrate taxa, suggesting that geomorphological conditions during the Late Miocene facilitated broadly simultaneous overwater waif dispersal of many South American lineages to the Lesser Antilles. These data provide an important baseline by which to further develop the Caribbean as a unique workshop for studying island evolution.     

Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.     

From Jumbo to Dumbo: Cranial Shape Changes in Elephants and Hippos During Phyletic Dwarfing

Members of the mammalian families Elephantidae and Hippopotamidae (extant and extinct elephants and hippos) include extinct dwarf species that display up to 98% decrease in body size compared to probable ancestral sources. In addition to differences in body mass, skulls of these species consistently display distinctive morphological changes, including major reduction of pneumatised areas in dwarf elephants and shortened muzzles in dwarf hippos. Here we build on previous studies of island dwarf species by conducting a geometric morphometric analysis of skull morphology and allometry in target taxa, living and extinct, and elaborate on the relation between skull size and body size. Our analysis indicates that skull size and body size within terrestrial placental mammals scale almost isometrically (PGLS major axis slope 0.906). Furthermore, skull shape in dwarf species differed from both their ancestors and the juveniles of extant species. In insular dwarf hippos, the skull was subject to considerable anatomical reorganisation in response to distinct selection pressures affecting early ontogeny (the “island syndrome”). By contrast, skull shape in adult insular dwarf elephants can be explained well by allometric effects; selection on size may thus have been the main driver of skull shape in dwarf elephants. We suggest that a tightly constrained growth trajectory, without major anatomical reorganization of the skull, allowed for flexible adaptations to changing environments and was one of the factors underlying the evolutionary success of insular dwarf elephants.     

Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha)

Caviomorphs are a clade of South American rodents recorded at least since the early Oligocene (> 31.5 Ma) that exhibit ample eco-morphological variation. It has been proposed that phylogenetic structure is more important than ecological factors for understanding mandibular shape variation in this clade. This was interpreted as a result of the long-standing evolutionary history of caviomorphs and the early divergence of major lineages. In this work, we test this hypothesis through the analysis of morphological variation in the mandible of living and extinct species and compare this information with that obtained through comparative phylogenetic analyses. Our results support the hypothesis of early origin of mandibular variation; moreover, they suggest the conservation of early differentiated morphologies, which could indicate the existence of constrained evolutionary diversification.     

Genomic and morphological data help uncover extinction‐in‐progress of an unsustainably traded hill myna radiation

The Asian songbird crisis which is currently unfolding in Southeast Asia has seen multiple bird taxa go extinct in the wild and even more slip into regional or local extinction over the span of only a few years. The hill mynas Gracula spp. are among its main victims, encompassing the Critically Endangered Nias Hill Myna Gracula [religiosa] robusta and other endangered populations across the West Sumatran Archipelago. Hill mynas are known to be present throughout this island chain but the taxonomic relationships of West Sumatran Gracula populations remain poorly understood. We hypothesized that the unique history of this island chain may have given rise to multiple distinct insular forms. Here we use genome‐wide DNA data in concert with morphological analyses to investigate the evolutionary distinctness of these taxa. Our results identify one taxon that is surprisingly distinct despite lacking recognition in most classifications, the ‘Simeulue Hill Myna’ (taxon miotera), and a range extension of the Nias Hill Myna. Despite their lack of recognition, Simeulue Hill Mynas are genomically and morphologically as unique as their Nias counterpart, in accordance with the lack of glacial land bridges between the island of Simeulue and mainland Sumatra. Simeulue Hill Mynas went extinct in the wild sometime within the last 2–3 years, and the rescue of the last captive individuals should now be the highest priority.     

Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.     

Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages

The ratio of species extinctions to introductions has been comparable for many insular assemblages, suggesting that introductions could have ‘compensated’ for extinctions. However, the capacity for introduced species to replace ecological roles and evolutionary history lost following extinction is unclear. We investigated changes in bird functional and phylogenetic diversity in the wake of extinctions and introductions across a sample of 32 islands worldwide. We found that extinct and introduced species have comparable functional and phylogenetic alpha diversity. However, this was distributed at different positions in functional space and in the phylogeny, indicating a ‘false compensation’. Introduced and extinct species did not have equivalent functional roles nor belong to similar lineages. This makes it unlikely that novel island biotas composed of introduced taxa will be able to maintain ecological roles and represent the evolutionary histories of pre‐disturbance assemblages and highlights the importance of evaluating changes in alpha and beta diversity concurrently.     

Mainland size variation informs predictive models of exceptional insular body size change in rodents

The tendency for island populations of mammalian taxa to diverge in body size from their mainland counterparts consistently in particular directions is both impressive for its regularity and, especially among rodents, troublesome for its exceptions. However, previous studies have largely ignored mainland body size variation, treating size differences of any magnitude as equally noteworthy. Here, we use distributions of mainland population body sizes to identify island populations as ‘extremely’ big or small, and we compare traits of extreme populations and their islands with those of island populations more typical in body size. We find that although insular rodents vary in the directions of body size change, ‘extreme’ populations tend towards gigantism. With classification tree methods, we develop a predictive model, which points to resource limitations as major drivers in the few cases of insular dwarfism. Highly successful in classifying our dataset, our model also successfully predicts change in untested cases.     

Phylogeny of snout butterflies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from the morphology of extant, fossil, and recently extinct taxa

Snout butterflies (Nymphalidae: Libytheinae) are morphologically one of the most unusual groups of Lepidoptera. Relationships among libytheines remain uncertain, especially in the placement of the recently extinct Libythea cinyras and two fossils, L. florissanti , and L. vagabunda . The aim of this study is to present the first phylogenetic hypothesis of Libytheinae utilizing all available morphological data from extant and extinct species. Forty-three parsimony-informative characters were coded, and the all-taxa analysis resulted in six most parsimonious trees (length 92 steps, CI = 0.66, RI = 0.82). The subfamily was resolved as monophyletic and was split into Old World and New World clades. Inclusion of extinct species with considerable missing data had little effect on relationships of extant taxa, although Bremer support values and jackknife frequencies generally decreased if extinct species were included. In order to preserve the monophyly of extant genera, two fossils are assigned to Libytheana for the first time ( L. florissanti comb. n. and L. vagabunda comb. n.). This study demonstrates the value of morphological data in phylogenetic analysis, and highlights the contribution that can be made by scoring extinct taxa and including them directly into the analysis.     

Systematics and biogeography of Indo-Pacific ground-doves

Ground-doves represent an insular bird radiation distributed across the Indo-Pacific. The radiation comprises sixteen extant species, two species believed to be extinct and six species known to be extinct. In the present study, we present a molecular phylogeny for all sixteen extant species, based on two mitochondrial markers. We demonstrate that the Gallicolumba as currently circumscribed is not monophyletic and recommend reinstalling the name Alopecoenas for a monophyletic radiation comprising ten extant species, distributed in New Guinea, the Lesser Sundas and Oceania. Gallicolumba remains the name for six species confined to New Guinea the Philippines and Sulawesi. Although our phylogenetic analyses fail to support a single origin for the remaining Gallicolumba species, we suspect that the addition of nuclear sequence data may alter this result. Because a number of ground-dove taxa have gone extinct, it is difficult to assess biogeographical patterns. However, the Alopecoenas clade has clearly colonized many remote oceanic islands rather recently, with several significant water crossings. The Gallicolumba radiation(s), on the other hand, is significantly older and it is possible that diversification within that group may in part have been shaped by plate tectonics and corresponding re-arrangements of land masses within the Philippine and Sulawesi region.     

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.     

Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards

Many of the classic examples of adaptive radiation, including Caribbean Anolis lizards, are found on islands. However, Anolis also exhibits substantial species richness and ecomorphological disparity on mainland Central and South America. We compared patterns and rates of morphological evolution to investigate whether, in fact, island Anolis are exceptionally diverse relative to their mainland counterparts. Quite the contrary, we found that rates and extent of diversification were comparable--Anolis adaptive radiation is not an island phenomenon. However, mainland and Caribbean anoles occupy different parts of morphological space; in independent colonizations of both island and mainland habitats, island anoles have evolved shorter limbs and better-developed toe pads. These patterns suggest that the two areas are on different evolutionary trajectories. The ecological causes of these differences are unknown, but may relate to differences in predation or competition among mainland and island communities.     

A new species of recently extinct rice rat (Megalomys) from Barbados

Recently extinct insular populations of oryzomyine rice rats (Cricetidae: Sigmodontinae) are known from across the Lesser Antilles, but most remain undescribed. Historical records of a possible now-extinct endemic rodent from Barbados are supported by presence of oryzomyine remains in Late Quaternary sites on the island, including several pre-Columbian Holocene archaeological sites. The Barbados oryzomyine is described as Megalomys georginae sp. nov., and is most closely related to species from the nearby islands of Martinique and St. Lucia, M. desmarestii and M. luciae. These species all display a zygomatic plate with its posterior margin level with the alveolus of M1, a divided anterocone on M1, and distinct anterolophids and metaflexids on m2 and m3, and are recovered as a monophyletic clade in morphological-molecular and morphology-only analyses. The new species differs from other Megalomys species in having the labial accessory root of M1 absent, a reduced anteromedian flexus on M1, two roots on m2 and m3, a supratrochlear foramen on the humerus, and in its much smaller body size. Other extinct Caribbean oryzomyines are not recovered in a monophyletic clade with Megalomys.     

Morphological divergence in giant fossil dormice

Insular gigantism—evolutionary increases in body size from small-bodied mainland ancestors—is a conceptually significant, but poorly studied, evolutionary phenomenon. Gigantism is widespread on Mediterranean islands, particularly among fossil and extant dormice. These include an extant giant population of Eliomys quercinus on Formentera, the giant Balearic genus †Hypnomys and the exceptionally large †Leithia melitensis of Pleistocene Sicily. We quantified patterns of cranial and mandibular shape and their relationships to head size (allometry) among mainland and insular dormouse populations, asking to what extent the morphology of island giants is explained by allometry. We find that gigantism in dormice is not simply an extrapolation of the allometric trajectory of their mainland relatives. Instead, a large portion of their distinctive cranial and mandibular morphology resulted from the population- or species-specific evolutionary shape changes. Our findings suggest that body size increases in insular giant dormice were accompanied by the evolutionary divergence of feeding adaptations. This complements other evidence of ecological divergence in these taxa, which span predominantly faunivorous to herbivorous diets. Our findings suggest that insular gigantism involves context-dependent phenotypic modifications, underscoring the highly distinctive nature of island faunas.     

Monophyly, phylogeny and systematic position of the †Synechodontiformes (Chondrichthyes, Neoselachii)

Klug, S. (2009). Monophyly, phylogeny and systematic position of the †Synechodontiformes (Chondrichthyes, Neoselachii). — Zoologica Scripta, 39 , 37–49.
Identifying the monophyly and systematic position of extinct sharks is one of the major challenges in reconstructing the phylogeny and evolutionary history of sharks in general. Although great progress has been accomplished in the last few decades with regard to resolving the interrelationships of living sharks, a comprehensive phylogeny identifying the systematic position of problematic or exclusively fossil taxa is still lacking. Fossil taxa traditionally assigned to synechodontiform sharks are very diverse with a fossil record extending back into the Palaeozoic but with uncertain inter- and intrarelationships. Here, phylogenetic analyses using robust cladistic principles are presented for the first time to evaluate the monophyly of this group, their intrarelationships and their systematic position within Neoselachii. According to the results of this study, taxa assigned to this group form a monophyletic clade, the †Synechodontiformes. This group is sister to all living sharks and displays a suite of neoselachian characters. Consequently, the concept of neoselachian systematics needs to be enlarged to include this completely extinct group, which is considered to represent stem-group neoselachians. The origin of modern sharks can be traced back into the Late Permian (250 Mya) based on the fossil record of †Synechodontiformes. The systematic position of batoids remains contradictory, which relates to the use of different data (molecular vs. morphological) in phylogentic analyses.     

First European evidence for transcontinental dispersal of Crocodylus (late Neogene of southern Italy)

It is generally assumed that the Neogene crocodylian fauna of Europe has been represented only by brevirostrine alligatoroid Diplocynodon and longirostrine false gharials ( Gavialosuchus and/or Tomistoma ), which became extinct prior to 6 Mya. Although several lines of evidence suggest that Crocodylus originated in Africa during the Miocene and then promptly dispersed to other continents, the occurrence of this genus in Europe has never been rigorously proven and the traditional palaeontological approach failed to identify a monophyletic group of fossil Crocodylus (simply leading to a proliferation of extinct taxa). The new remains reported here, from an endemic insular fauna from southern Italy, Late Messinian to earliest Pliocene in age (5–6 million years old), represent the youngest European crocodylian, and allow, for the first time in a phylogenetic context, an unambiguous demonstration that Crocodylus dispersed into Europe, possibly during the Tortonian. If the peculiar morphology of the medial maxillary edge is interpreted as evidence for a medial dorsal boss, the southern Italian Crocodylus could be related to C. checchiai from the late Neogene of Libya. The presence of this African immigrant in Europe confirms the role of climate change for faunal dispersal and island colonization.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 293–307.     

Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards

Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism). The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces) longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a “life raft” preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.     

Evolutionary relationships, interisland biogeography, and molecular evolution in the Hawaiian violets (Viola: Violaceae)

The endemic Hawaiian flora offers remarkable opportunities to study the patterns of plant morphological and molecular evolution. The Hawaiian violets are a monophyletic lineage of nine taxa distributed across six main islands of the Hawaiian archipelago. To describe the evolutionary relationships, biogeography, and molecular evolution rates of the Hawaiian violets, we conducted a phylogenetic study using nuclear rDNA internal transcribed spacer sequences from specimens of each species. Parsimony, maximum likelihood (ML), and Bayesian inference reconstructions of island colonization and radiation strongly suggest that the Hawaiian violets first colonized the Maui Nui Complex, quickly radiated to Kaua'i and O'ahu, and recently dispersed to Hawai'i. The lineage consists of "wet" and "dry" clades restricted to distinct precipitation regimes. The ML and Bayesian inference reconstructions of shifts in habitat, habit, and leaf shape indicate that ecologically analogous taxa have undergone parallel evolution in leaf morphology and habit. This parallel evolution correlates with shifts to specialized habitats. Relative rate tests showed that woody and herbaceous sister species possess equal molecular evolution rates. The incongruity of molecular evolution rates in taxa on younger islands suggests that these rates may not be determined by growth form (or lifespan) alone, but may be influenced by complex dispersal events.     

Molecular phylogeny and diversification of freshwater shrimps (Decapoda, Atyidae, Caridina) from ancient Lake Poso (Sulawesi, Indonesia)--the importance of being colourful

Ancient Lake Poso on the Indonesian island Sulawesi hosts a highly diverse endemic fauna, including a small species flock of atyid Caridina shrimps, which are characterized by conspicuous colour patterns. We used a mtDNA based molecular phylogeny to test the assumption of a monophyletic origin and intralacustrine radiation of the species flock and to assess the species specificity of some colour morphs. Our data reveal a rapid radiation of Caridina in the entire Poso drainage system, but provide no strong evidence for a monophyletic radiation of the lake species. Nevertheless each lacustrine species shows a varying degree of substrate or trophic specialization, usually considered a hallmark of adaptive radiation. Two distinct colour forms previously attributed to a single species, C. ensifera, lack distinguishing qualitative morphological characters, but are shown to be two different species. In contrast, morphologically rather distinct lake species lacking specific colour patterns may be hybridizing with riverine taxa. These results suggest that colour may play a similar role in species recognition and possibly speciation in ancient lake Caridina as hypothesized, e.g. for some African cichlids.