69 research outputs found
Quantitative sexing (Q-sexing) technique for animal sex-determination based on X chromosome-linked loci: Empirical evidence from the Siberian tiger
Here we report a mammal sexing procedure based on the detection of quantitative differences between females and males in the X-linked loci (quantitative sexing, Q-sexing). This novel technique was validated using samples from Siberian tigers (Panthera tigris altaica) whose sexes were known. The Q-sexing technique relies on the fact that amplifications proceeding exclusively from the two X chromosomes in a female mammal should reach the threshold cycle (CT) in a real-time quantitative real time polymerase chain reaction (qPCR) assay sooner than amplifications from the single male X chromosome. Nevertheless, given that the amplification efficiency may vary between samples, results have to be calibrated to a marker that does not vary in copy number between the sexes (for example, an autosomal-linked locus). For this purpose we used quantitative real time polymerase chain reaction (RT qPCR) assays to quantify the amount of three specific Siberian tiger microsatellite markers (X-/Y- and autosomal-linked loci) in individual samples in order to determine the sex of an animal. A difference of one CT between the X and the autosome-linked loci was detected in males, but no such difference was present in female samples. The Q-sexing technique unambiguously separates female from male Siberian tigers. The future of RT qPCR is bright as technology is becoming ever more rapid, cost-effective, easier to use and capable of processing higher throughputs. Thus, we expect that our novel technique for animal sexing will have a wide applicability, although further studies are still needed to adapt it to other animal species using specific primers.Key words: Polymerase chain reaction (PCR), quantitative real time polymerase chain reaction (qPCR), quantitative sexing, Siberian tiger
Whole genome sequencing and methylome analysis of the wild guinea pig
Abstract Background: DNA methylation is a heritable mechanism that acts in response to environmental changes, lifestyle and diseases by influencing gene expression in eukaryotes. Epigenetic studies of wild organisms are mandatory to understand their role in e.g. adaptational processes in the great variety of ecological niches. However, strategies to address those questions on a methylome scale are widely missing. In this study we present such a strategy and describe a whole genome sequence and methylome analysis of the wild guinea pig
an island endemic forest specialist and a widespread habitat generalist
Background. The bay cat Catopuma badia is endemic to Borneo, whereas its
sister species the Asian golden cat Catopuma temminckii is distributed from
the Himalayas and southern China through Indochina, Peninsular Malaysia and
Sumatra. Based on morphological data, up to five subspecies of the Asian
golden cat have been recognized, but a taxonomic assessment, including
molecular data and morphological characters, is still lacking. Results. We
combined molecular data (whole mitochondrial genomes), morphological data
(pelage) and species distribution projections (up to the Late Pleistocene) to
infer how environmental changes may have influenced the distribution of these
sister species over the past 120â000 years. The molecular analysis was based
on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly
from archival samples. Our molecular data suggested a time of split between
the two species approximately 3.16âMa and revealed very low nucleotide
diversity within the Asian golden cat population, which supports recent
expansion of the population. Discussion. The low nucleotide diversity
suggested a population bottleneck in the Asian golden cat, possibly caused by
the eruption of the Toba volcano in Northern Sumatra (approx. 74âkya),
followed by a continuous population expansion in the Late Pleistocene/Early
Holocene. Species distribution projections, the reconstruction of the
demographic history, a genetic isolation-by-distance pattern and a gradual
variation of pelage pattern support the hypothesis of a post-Toba population
expansion of the Asian golden cat from south China/Indochina to Peninsular
Malaysia and Sumatra. Our findings reject the current classification of five
subspecies for the Asian golden cat, but instead support either a monotypic
species or one comprising two subspecies: (i) the Sunda golden cat,
distributed south of the Isthmus of Kra: C. t. temminckii and (ii)
Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the
Isthmus: C. t. moormensis
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Adaptive responses of animals to climate change are most likely insufficient
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species. © 2019, The Author(s)
Adaptive responses of animals to climate change are most likely insufficient
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.Peer reviewe
A methodological approach for non-invasive sampling for population size estimates in wild boars (Sus scrofa
Abstract Composite microsatellite genotypes were determined at five loci from 35 tissue-sampled wild boars and used as reference genotypes to estimate both allelic dropout rate and false allele rate in comparison to genotypes from scats and hair strands of the same animals. These rates allow to assess the genotyping reliability when only noninvasively collected material is available. Polymerase chain reaction (PCR) amplification from scats was often corrupted by inhibitors and worked poorly, whereas genotyping success in hair samples was high. Body region of hair origin had no influence on PCR suitability, whereas the type of hair had. We recommend the use of bristles. PCR conditions were optimized for single-hair (bristle) genotyping
A methodological approach for non-invasive sampling for population size estimates in wild boars (Sus scrofa
Abstract Composite microsatellite genotypes were determined at five loci from 35 tissue-sampled wild boars and used as reference genotypes to estimate both allelic dropout rate and false allele rate in comparison to genotypes from scats and hair strands of the same animals. These rates allow to assess the genotyping reliability when only noninvasively collected material is available. Polymerase chain reaction (PCR) amplification from scats was often corrupted by inhibitors and worked poorly, whereas genotyping success in hair samples was high. Body region of hair origin had no influence on PCR suitability, whereas the type of hair had. We recommend the use of bristles. PCR conditions were optimized for single-hair (bristle) genotyping
The complete mitochondrial genome of the meerkat (Suricata suricatta) and its phylogenetic relationship with other feliform species
The meerkat, Suricata suricatta, is a highly social member of the mongoose family (Herpestidae) and the only extant species of the genus Suricata. We present the first complete mitochondrial genome of the meerkat, assembled with a seed-and-extend algorithm using three closely related species as references. Phylogenetic analyses using 22 mitochondrial genome sequences confirm the position of meerkat within the Herpestidae family and the Feliformia, a suborder of Carnivora, with high support values. This position is in good agreement with formerly conducted studies based on a small number of mitochondrial and nuclear gene fragments. Our complete mitochondrial genome represents a valuable resource for further phylogenetic studies, especially of the underrepresented members of the Herpestidae family
Evolution and phylogeny of old world deer
The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51 ± 0.1 species per million years (my) over roughly the last 6 mya
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