Evolution of the extinct Sabretooths and the American cheetah-like cat

The sabretooths (Smilodon and Homotherium) and the American cheetah-like cat (Miracinonyx) were the top predators in Late Pleistocene America, but became extinct about 13 thousand years ago. As the evolutionary history of these taxa remains poorly understood , we analysed their phylogenetic relationship to extant felids. In contrast to previous molecular studies , our results show that the sabretooths diverge early and are not closely related to any living cats. This supports their morphological placement in a separate subfamily (Machairodontinae). Despite its remarkable morphological similarity to the African cheetah (Acinonyx jubatus), Miracinonyx appears to have evolved from a puma-like ancestor, presumably in response to similar ecological pressures.

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography

The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction �600 years ago. The phylogeny and evolutionary history of this morphologically diverse order has remained controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20–30 Ma. The data reveal that the patterns of genetic diversity within and between differentmoaclades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5–8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

The aquatic biota of the now extinct lacustrine complex of the Mexico basin

The commonest organisms of the original Mexico lake complex are listed, including those that exist today in the Lago Viejo. In addition, a brief hydraulic history of this endorheic basin is given.

Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data.

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.

Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath hen.

Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens.

Palaeobiology of an extinct Ice Age mammal: Stable isotope and cementum analysis of giant deer teeth

The extinct giant deer, Megaloceros giganteus, is among the largest and most famous of the cervids. Megaloceros remains have been uncovered across Europe and western Asia. but the highest concentrations come from Irish bogs and caves Although Megaloceros has enjoyed a great deal of attention over the centuries, paleobiological study has focused oil morphometric and distributional work until now. This paper presents quantitative data that have implications for understanding its sudden extirpation in western Europe during a period of global climate change approximately 10.600 C-14 years ago (ca 12,500 calendar years BP). We report here the first stable isotope analysis of giant deer teeth. which we combine with dental cementum accretion in order to document age, diet and life-history seasonality from birth until death Enamel delta C-13 and delta O-18 measured in the second and third molars from seven individual giant deer Suggest a grass and forbbased diet supplemented with browse in a deteriorating. possibly water-stressed, environment, and a season of birth around spring/early summer Cementurm data indicate that the ages of the specimens ranged from 6.5 to 14 years and that they possessed mature antlers by autumn, similar to extant cervids. In addition. the possibility for combining these two techniques in future mammalian paleoccological studies is considered. The data presented in this study imply that Megoloceros would have indeed been vulnerable to extirpation during the terminal Pleistocene in Ireland. and this information is relevant to understanding the broader pattern of its extinction.

Ecological dynamics of extinct species in empty habitat networks. 1. The role of habitat pattern and quantity, stochasticity and dispersal

We examined a remnant host plant (Primula veris L.) habitat network that was last inhabited by the rare butterfly Hamearis lucina L. in north Wales in 1943, to assess the relative contribution of several spatial parameters to its regional extinction. We first examined relationships between P. veris characteristics and H. lucina eggs in surviving H. lucina populations, and used these to predict the suitability and potential carrying capacity of the habitat network in north Wales. This resulted in an estimate of roughly 4500 eggs (ca 227 adults). We developed a discrete space, discrete time metapopulation model to evaluate the relative contribution of dispersal distance, habitat and environmental stochasticity as possible causes of extinction. We simulated the potential persistence of the butterfly in the current network as well as in three artificial (historical and present) habitat networks that differed in the quantity (current and X3) and fragmentation of the habitat (current and aggregated). We identified that reduced habitat quantity and increased isolation would have increased the probability of regional extinction, in conjunction with environmental stochasticity and H. lucina's dispersal distance. This general trend did not change in a qualitative manner when we modified the ability of dispersing females to stay in, and find suitable habitats (by changing the size of the grid cells used in the model). Contrary to most metapopulation model predictions, system persistence declined with increasing migration rate, suggesting that the mortality of migrating individuals in fragmented landscapes may pose significant risks to system-wide persistence. Based on model predictions for the present landscape we argue that a major programme of habitat restoration would be required for a re-established metapopulation to persist for > 100 years.

Ecological dynamics of extinct species in empty habitat networks. 2. The role of host plant dynamics

This paper explores the relative effects of host plant dynamics and butterfly-related parameters on butterfly persistence. It considers an empty habitat network where a rare butterfly (Cupido minimus) became extinct in 1939 in part of its historical range in north Wales, UK. Surviving populations of the butterfly in southern Britain were visited to assess use of its host plant (Anthyllis vulneraria) in order to calibrate habitat suitability and carrying capacity in the empty network in north Wales. These data were used to deduce that only a portion ( similar to 19%) of the host plant network from north Wales was likely to be highly suitable for oviposition. Nonetheless, roughly 65,460 eggs (3273 adult equivalents) could be expected to be laid in north Wales, were the empty network to be populated at the same levels as observed on comparable plants in surviving populations elsewhere. Simulated metapopulations of C. minimus in the empty network revealed that time to extinction and patch occupancy were significantly influenced by carrying capacity, butterfly mean dispersal distance and environmental stochasticity, although for most reasonable parameter values, the model system persisted. Simulation outputs differed greatly when host plant dynamics was incorporated into the modelled butterfly dynamics. Cupido minimus usually went extinct when host plant were at low densities. In these simulations host plant dynamics appeared to be the most important determinant of the butterfly's regional extirpation. Modelling the outcome of a reintroduction programme to C. minimus variation at high quality locations, revealed that 65% of systems survived at least 100 years. Given the current amount of resources of the north Wales landscape, the persistence of C. minimus under a realistic reintroduction programme has a good chance of being successful, if carried out in conjunction with a host plant management programme.

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Background: Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods: 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results: Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions: Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed ‘Algarvia’ (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds – Arouquesa (AR), Barrosa˜ (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.