Bones of recent mammals in the Amboseli Basin, southern Kenya, exhibit distinctive weathering characteristics that can be related to the time since death and to the local conditions of temperature, humidity and soil chemistry. A categorization of weathering characteristics into six stages, recognizable on descriptive criteria, provides a basis for investigation of weathering rates and processes. The time necessary to achieve each successive weathering stage has been calibrated using known-age carcasses. Most bones decompose beyond recognition in 10 to 15 yr. Bones of animals under 100 kg and juveniles appear to weather more rapidly than bones of large animals or adults. Small-scale rather than widespread environmental factors seem to have greatest influence on weathering characteristics and rates. Bone weathering is potentially valuable as evidence for the period of time represented in recent or fossil bone assemblages, in- cluding those on archeological sites, and may also be an important tool in censusing populations of animals in modern ecosystems.

Taphonomic and Ecologic Information Form Bone Weathering

Climate change in the past has led to significant changes in species' distributions. However, how individual species respond to climate change depends largely on their adaptations and environmental tolerances. In the Quaternary, temperate-adapted taxa are in general confined to refugia during glacials while cold-adapted taxa are in refugia during interglacials. In the Northern Hemisphere, evidence appears to be mounting that in addition to traditional southern refugia for temperate species, cryptic refugia existed in the North during glacials. Equivalent cryptic southern refugia, to the south of the more conventional high-latitude polar refugia, exist in montane areas during periods of warm climate, such as the current interglacial. There is also a continental/oceanic longitudinal gradient, which should be included in a more complete consideration of the interaction between species ranges and climates. Overall, it seems clear that there is large variation in both the size of refugia and the duration during which species are confined to them. This has implications for the role of refugia in the evolution of species and their genetic diversity.

https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2009.1272

Refugia revisited: individualistic responses of species in space and time

The glacial episodes of the Quaternary (2.6 million years ago–present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.

/pdf/phylogeographic-insights-into-cryptic-glacial-refugia-1ephre68rp.pdf

Phylogeographic insights into cryptic glacial refugia.

We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson‐Dobzhansky‐ Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be .2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these ‘‘morphologically cryptic genetic species’’ are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F1s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is ‘‘reproductively isolated species.’’ Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen‐based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.

/pdf/speciation-in-mammals-and-the-genetic-species-concept-2jfs20085j.pdf

Speciation in mammals and the genetic species concept

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0000563&type=printable

Locating pleistocene refugia: comparing phylogeographic and ecological niche model predictions.

1Glacial refugia were core areas for the survival of temperate species during unfavourable environmental conditions and were the sources of postglacial recolonizations. Unfortunately, the locations of glacial refugia of animals and plants are usually described by models, without reference to facts about real geographical ranges at that time.
2Careful consideration of the faunal assemblages of archaeological sites from the Younger Palaeolithic, which are precisely dated to the Last Glacial Maximum (LGM), gives indications about the distribution of species during the LGM (23 000–16 000 bp) and provides evidence for the locations of glacial refugia for mammalian species in Europe.
3In Europe, 47 LGM sites, dating from 23 000 to 16 000 bp and containing typical temperate mammal species, have been described. The geographical range of these archaeological sites clearly shows a distribution which differs from the hypothesized traditional refuge areas of the temperate fauna. A considerable number of sites situated in the Dordogne in south-western France and the Carpathian region contain records of red deer Cervus elaphus, roe deer Capreolus capreolus, wild boar Sus scrofa and red fox Vulpes vulpes.
4The faunal composition of the majority of the evaluated Palaeolithic sites in the southern European peninsulas (with the exception of Greece), as well as France and the Carpathian region, indicates the co-occurrence of these temperate species with cold-adapted faunal elements such as mammoth Mammuthus primigenius and/or reindeer Rangifer tarandus.
5The survival of species in Central European refugia would have significant consequences for phylogeography and would be revealed by the dominant distribution of haplotypes, originating from this region. A Carpathian refuge could also be the reason for the very early records of small mammals or mustelids from the Late-Glacial or Interstadials before the LGM in regions like southern Germany.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2907.2006.00093.x

Glacial refugia of mammals in Europe: evidence from fossil records

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences.

Late Quaternary rodents of Poland with special reference to morphotype dentition analysis of voles

Analysis of dental characters of Chionomys supported by a comparison with biochemical and karyological criteria shows its isolation from Microtus (sensu stricto). Snow voles (Chionomys) consist of two lineages developed separately since the Lower Biharian. The first one has appeared and evolved in Europe (Ch. nivalis lineage) while the second is probably of the Near East or Caucasus origin (Ch. roberti-gud lineage). Variation in dental characters of extant Ch. nivalis permit to reconstruct affinities between particular populations comparable in this respect with biochemical data. Fossil species traditionally included in the Chinomys group (Microtus malei, M. nivaloides, M. nivalinus, M. ratticepoides) seem to belong to Microtus sensu stricto.

/pdf/systematics-geographic-variation-and-evolution-of-snow-voles-451t07scv0.pdf

Adam Nadachowski

Papers

Glacial refugia of mammals in Europe: evidence from fossil records

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences.

Late Quaternary rodents of Poland with special reference to morphotype dentition analysis of voles

Systematics, geographic variation, and evolution of snow voles ( Chionomys ) based on dental characters

Pleistocene Voles (Arvicolidae) of the Ukraine