LGDMSNO09700
May 4, 2009
Journal of Heredity
NB: please do not reformat reference w/ EndNote without checking Bob’s edits to the
lit. cited section.
Genome 10K: A Proposition to Obtain Whole Genome Sequence
for 10,000 Vertebrate Species
Genome 10K Community of Scientists
Table of Contents
Table of Contents ............................................................ Error! Bookmark not defined.
Abstract ........................................................................................................................... 3
Introduction ..................................................................................................................... 4
Proposal .......................................................................................................................... 7
Mammals......................................................................................................................... 9
Birds .............................................................................................................................. 10
Reptiles ......................................................................................................................... 11
Amphibians ................................................................................................................... 12
Fish ............................................................................................................................... 13
Discussion ..................................................................................................................... 15
Methods: ....................................................................................................................... 18
Appendix 1: Policy issues.............................................................................................. 19
Appendix 2: Detailed table of classes, orders, families, genera and species ................ 20
Appendix 3: Technological issues ................................................................................. 24
Authors: ......................................................................................................................... 25
References: ................................................................................................................... 26
Table 1: Vertebrate taxa ................................................................................................ 29
Table 2: List of collections and participating institutions (Fill this in) .............................. 30
Figure legends (need these) (Fill in references) ............................................................ 33
Figure 1: A phylogenetic view of the vertebrate subclass.............................................. 34
Figure 2: The mammalian radiations ............................................................................. 35
Figure 3: The birds of the world ..................................................................................... 36
Figure 4: The reptiles of today ....................................................................................... 37
Figure 5: The amphibians’ phylogeny............................................................................ 38
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Abstract
The human genome project was recently complemented by whole genome
sequencing assessment of 32 mammals and 24 non-mammal vertebrate species
suitable for comparative genomic analyses. Here, we anticipate the precipitous drop in
sequencing costs and the development of greater annotation technology by proposing
to create a collection of tissue and DNA specimens for 10,000 vertebrate species
specifically designated for whole genome sequencing in the very near future. For this
purpose we, the G10K Community of Scientists, assemble and allocate a collection of
some 16,000 representative vertebrate species spanning evolutionary diversity across
living mammals, birds, reptiles, amphibians and fishes (circa 60,000 living species).
With this resource, the biological science community for genome sequence
assessment may now pursue the opportunity to usher in a new era of investigation in
the biological sciences, embark upon the most comprehensive study of biological
evolution ever attempted, and invigorate genomic inference into every aspect of
vertebrate biological enquiry.
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Introduction
The bold insight behind the success of the human genome project was that,
while vast, the roughly three billion bits of digital information specifying the total genetic
heritage of an individual is finite and might, with dedicated resolve, be brought within the
reach of our technology [1] [2] [3]. The number of living species is similarly vast,
estimated to be between 106 and 108 for all metazoans, and approximately 6 x 104 for
the subphylum vertebrata, the evolutionarily closest relatives to humans. With that same
unity of purpose, we can now contemplate reading the genetic heritage of all species,
beginning with the vertebrates. The feasibility of a “Genome 10K” project to catalog the
diversity of vertebrate genomes requires but one more order of magnitude reduction in
the cost of DNA sequencing, following the four orders of magnitude reduction we have
seen in the last 10 years. It is time to prepare for this undertaking.
Living vertebrate species derive from a common ancestor that lived roughly 500
million years ago (Ma), near the time of the Cambrian explosion of animal life. Because
a core repertoire of about 10,000 genes in a genome of about a billion bases is seen in
multiple, deeply-branching vertebrates and close deuterostome out-groups, we may
surmise that the haploid genome of the common vertebrate ancestor was already highly
sophisticated; consisting of 108 - 109 bases specifying a body plan that includes
segmented muscles derived from somites, a notochord and dorsal hollow neural tube
differentiating into primitive forbrain, midbrain, hindbrain and spinal chord structures,
basic endocrine functions encoded in distant precursors to the thyroid, pancreas and
other vertebrate organs, and a highly sophisticated innate immune system [4-8] [9] [10].
In the descent of the living vertebrates, the roughly 108 bases in the functional DNA
segments that specify these sophisticated features, along with more fundamental
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biological processes, encountered on average more than 30 substitutions per nucleotide
site, the outcome of trillions of natural evolutionary experiments. These and other
genetic changes, including rearrangements, duplications and losses, spawned the
diversity of vertebrate forms that inhabit the planet today. A Genome 10K project
explicitly detailing these genetic changes will provide an essential reference resource
for an emerging new synthesis of molecular, organismic, developmental and
evolutionary biology to explore the forms of life, just as the human genome project has
provided an essential reference resource for a new biomedicine.
Beyond elaborations of ancient biochemical and developmental pathways,
vertebrate evolution is characterized by stunning innovations, including adaptive
immunity, multi-chambered hearts, cartilage, bones and teeth, an internal skeleton that
has given rise to the largest aquatic and terrestrial animals on the planet, and
specialized endocrine organs such as the pancreas, thyroid, thymus, pituitary, adrenal
and pineal glands [11]. At the cellular level, the neural crest, sometimes referred to as a
fourth germ layer, is unique to vertebrates and gives rise to a great variety of structures,
including some skeletal elements, tendons and smooth muscle, neurons and glia of the
autonomic nervous system and aspects of the sensory systems, melanocytes in the
skin, dentin in the teeth, parts of endocrine system organs, and connective tissue in the
heart [12, 13]. Sophisticated vertebrate sensory, neuroanatomical and behavioral
elaborations coupled with often dramatic anatomical changes allowed exploitation of
oceanic, terrestrial, and atmospheric ecological niches. Anticipated details of
expansions and losses of specific gene families revealed by the Genome 10K project
will provide profound insights into the molecular mechanisms behind these
extraordinary innovations.
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Adaptive changes in non-coding regulatory DNA also play a fundamental role in
vertebrate evolution and its understanding represents an even greater challenge.
Almost no part of the non-coding vertebrate gene regulatory apparatus bears any
discernable resemblance at the DNA level to analogous systems in our deuterostome
distant cousins, yet the apparatus occupies the majority of the bases we find to be
under selection in vertebrate genomes, and is hypothesized to be the major source of
evolutionary innovation within vertebrate subclades [14] [15] [6] [16]. The origins and
evolutionary trajectory of the subset of non-coding functional elements under the
strongest stabilizing selection can be traced deep into the vertebrate tree [17], in many
cases to its very root, while other non-coding functional elements have uniquely arisen
at the base of a particular class, order or family of vertebrate species. Within vertebrate
clades that evolved from a common ancestor in the last 108 million years, such as
mammals (5000 species), modern birds (10,000 species), Anura (5,700 frog and toad
species), Acanthomorpha (16,000 fish species), snakes (3000 species), geckos (1000
species) and skinks (1300 species), evolutionary coalescence to a common ancestral
DNA segment can be reliably determined even for segments of non-coding evolving
DNA. This enables detailed studies of base-by-base evolutionary changes throughout
the genome, in both coding and non-coding DNA [14]. With an estimated neutral branch
length of about 20 substitutions per site within such clades, the Genome 10K project
provides enormous depth of genome-wide sequence variation to address critical
hypotheses concerning the origin and evolution of functional non-coding DNA segments
and their role in molding physiological and developmental definitions of living animal
species.
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Proposal
To this end, we propose to assemble a “virtual collection” of frozen or otherwise
suitably preserved tissues or DNA samples representing on the order of 10,000 extant
vertebrate species as well as some recently extinct species that are amenable to
genomic sequencing (Table 1). This collection represents combined specimen materials
from at least 43 participating institutions (Table 2). In most cases, we collected both
male and female samples, and for certain species, several samples reflecting
geographic diversity and/or diversity within localized populations.
Tissues in genetic resources collections have been stored by different methods,
which yield varying results with regard to DNA quality [18]. Many tissues that are
sampled from the field may be left at ambient temperatures for several hours before
they are finally frozen in liquid nitrogen and subsequently stored there or at -80°C.
Nonetheless, many of these tissues still yield high quality DNA [19]. In other cases,
non-cryogenic field buffers [20] are used, although with varying results. In addition to
DNA quality, permit and species validation are also important issues (Appendix 1). We
follow four general guidelines for Genome 10K sample collection.

We seek 10μg of genomic DNA or about 0.5g of frozen tissue for each target
species.

Tissues may be field preserved in liquid nitrogen, ethanol, or DMSO. Initial
preservation in liquid nitrogen is strongly recommended for new acquisitions when field
conditions permit. Transport in liquid nitrogen or dry ice is encouraged. Tissues should
be stored in -80ºC freezers or in liquid nitrogen.

Tissues should be documented with voucher specimens when feasible.
Preserved carcasses are preferred; photo vouchers acceptable and DNA Barcode
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information will be collected for all (DNA barcode reference). In the case of rare or
endangered species, a tissue sample, locality, ID by competent biologist and DNA
Barcode confirmation or listing in the International Species Information System is
nominally acceptable.

All specimens used in the G10K project will be obtained and transported in
accord with local and international statutes regulating the collection, use, and transport
of biological specimens.
In addition to samples for DNA extraction, we included 1,006 cryopreserved
fibroblast cell lines derived from 602 different vertebrate species, primarily mammals,
but include representatives of 300 taxa comprising 42 families of non-mammalian
amniotes and one amphibian species, which provides an additional window into the
unique cell biology of these species. With the recent development of transformation
techniques to create induced pluripotent stem (iPS) cells from fibroblast lines [21, 22]
[23] [24], the potential of cell line studies is greatly expanded. While it is still unclear how
well current cell line generation methods can be extended to all vertebrate clades [25]
[26], we propose to initiate primary fibroblast cell cultures for as many species as
possible, with a target of at least 2,000 diverse species, as corollary to the Genome 10K
project. These cell cultures, along with cDNA derived from primary tissues, will provide
direct access to gene expression and regulation in the vertebrate species we catalog
and provide a renewable experimental resource to complement the Genome 10K
genome sequences. For at least one species of each vertebrate Order, we propose to
assemble additional genomic resources, including physical maps and a BAC library, cell
lines, and primary tissues for transcriptome analysis. For these species, we will also
sequence multiple individuals to assess within-species diversity, including members of
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both sexes to assess sex chromosome differences. A resource of this magnitude would
help catalyze a much-needed extension of experimental molecular biology beyond the
very limited set of model organisms it currently explores.
The Genome 10K species collection will include tissue/DNA specimens from five
major taxonomic groups: mammals, birds, amphibians, non-avian reptiles and fishes
(Table 1).
Mammals
Mammals contain a morphologically and behaviorally diverse assemblage of
approximately 5,400 species distributed in three major lineages: monotremes (platypus
and echidnas—5 species), marsupials (~330 species, including the koala, kangaroos,
opossums, etc.), and the speciose eutherian, or placental mammals (~5,000 species).
The Genome 10K collections contain exemplars of all 139 families and we have
access to ~90% of non-muroid and non-sciurid rodent genera and non-vespertilionid bat
genera (Appendix 2, mammals). Ultimately, we will target all 1,200–1,300 genera.
Additional sampling will be applied to deeply divergent, and especially
endangered, or EDGE (Evolutionary Distinct and Endangered) species, including all
species of Zaglossus (echidna), Cuban and Hispaniolan Solenodon, saddle-baked tapir,
aardvark, and others. For fundamental biological investigation, it is a high priority to
sequence “extremophiles”, such as deep sea divers, high elevation species, aquatic
versus terrestrial taxa, species spanning the range of brain size, body size, and
morphological convergence as well as aquatic species, gliders, lifespan extremes,
nocturnal/diurnals, species with distinct sensory modalities, such as echolocation, and
social versus solitary species with diverse mating systems and varying levels of paternal
care and care from the social group.
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Capturing wide ecological diversity holds great potential in identifying the
genomic changes underlying the major mammalian anatomical and behavioral
transformations including the dramatic changes underlying the evolution of advanced
social and eusocial systems. We project approximately 3,000 of the 5,400 living
mammal species.
Birds
Like eutherian mammals, modern birds (Neornithes) arose in the Late
Cretaceous and diversified soon after the KT extinction event, 65 Ma. Since then, birds
have dispersed across the globe and now occupy most of Earth's habitats and diverse
ecosystems representing a wide array of functional lifestyles. At this time, we know very
little about the genetic and developmental underpinnings of this biological diversity, but
we expect that many key questions can and will be addressed as whole genome
sequences are accumulated and interpreted.
During recent decades, the avian systematic community built large frozen tissue
collections that house high quality samples of a substantial portion of avian diversity.
These collections provide an essential resource for future genomic analyses of avian
structural, functional, and behavioral diversity. With representation from 15 natural
history collections distributed globally, the Genome 10K collection includes specimens
from 100% of the 27 orders, 87% of the 205 families, 71% of the 2,172 genera and 50%
of the 9,723 species of birds (Appendix 2, birds). Every order is represented in multiple
collections, as are all but 5 families and all but 104 genera, which is important for
ensuring at least one sample of high quality. We plan to sequence both sexes for many
lineages, especially the ratite birds, many of which have apparently monomorphic or
near-monomorphic sex chromosomes. Sampling each genus may result in
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oversampling of some avian orders and families (such as the extremely diverse
passerines or hummingbirds), but we will strive to capture maximal phylogenetic
coverage across all bird species.
Non-avian Reptiles
Non-avian reptile diversity includes snakes, lizards, turtles, crocodilians, and one
or two species of tuatara. Because the traditional view of interfamilial relationships
(based on morphology) differs appreciably with recent molecular phylogenies and the
molecular phylogenies with one another, major issues such as the origin of snakes
(which are clearly nested within lizards) remain controversial (NEW REF: Fry et al.
2006). In addition to these uncertainties, the phylogenetic relationships within and
among the major groups of reptiles (i.e., families) are often unstable, especially as this
relates to “colubroid” snakes and speciose assemblages of lizards. Major revisions
occur within many groups, such as the geckos, where additional families are now
recognized. Following online databases and Townsend et al. (2004) [27], reptile
diversity is distributed among the following groupings: Snakes are divided among 19
families, 477 genera, and 3,048 species. Lizards are comprised of 33 families, 490
genera, and 5,057 species. Turtle diversity is divided among 13 families, 91 genera, and
313 species (NEW REF: Turtle Taxonomy working group, 2007). Crocodiles include 23
species divided among 7 genera in 3 taxonomic families. The tuatara is the only extant
member of the formerly diverse and widespread Rhyncocephalia. Total reptile diversity
therefore includes 70 families, 1,067 genera, and 8,443 species. The Genome 10K
collection has 67%, 34% and 10% of these, respectively (Appendix 2, reptiles).
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Amphibians
The Class Amphibia is divided into three orders: Anura (frogs), Caudata
(salamanders) and Gymnophiona (caecilians), derived from a common ancestor 260 Ma
and representing the only three surviving lineages from a much greater diversity that
existed before the Permian extinction 250 Ma (NEW REF: Marjanović, D. and M. Laurin,
Fossils, molecules, divergence times, and the origin of lissamphibians. Systematic
Biology, 2007. 56: p. 369-388.). These major clades contain 5,773 frog species, 580
salamander species, and 176 caecilian species, respectively. Amphibian taxonomy is
currently in a state of flux, if not disarray, with different groups of systematists making
frequent and often conflicting changes. Although controversial, we summarize
amphibian diversity and tissue holdings for higher taxonomic groups (Appendix 2,
amphibians) following the Amphibian Species of the World data base [41]. This
reference largely follows the taxonomy of Frost et al. (2006) [29], but also incorporates
subsequent changes. This schema tends to split groups, adding more families and
genera, which helps us identify the major lineages using the standard ranks of Linnean
classification. This taxonomy contains 61 families of amphibians shared among the
three orders, containing a total of 510 genera and 6,260 species. The Genome 10K
collection contains a total of 394 species (6%), 144 genera (28%), and 45 families
(74%) (Appendix 2, amphibians).
Amphibians are notorious for their morphological homoplasy due to
developmental constraints [citation in COMMENT] as well as spectacular adaptativa
convergences in morphology [citation in COMMENT], behavior, and development, e.g.,
roughly ten independent evolutionary origins of direct development from an ancestral
biphasic life history[citation in COMMENT]. Perhaps the most striking example is the
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convergent evolution in toxicity, coloration and parental care between mantellid frogs of
Madagascar and dendrobatid frogs in the Neotropics, as well as repeated parallel
evolution of these traits within each of these two taxonomic families [2 citations given in
COMMENT]. Such homoplasies have wrecked havoc on amphibian taxonomy but offer
marvelous opportunities to study the genetic basis of the repeated evolution of complex
traits involved in both morphological and behavioral evolution.
Collectively, amphibians are of global conservation concern [30], most recently
because of pathogenic affects of a chytrid fungus, Batrachochytrium dendrobatidis [see
comment for new citation]. Habitat loss, pollutants, pesticides, herbicides, fertilizers and
climatic changes are further contributing to their current demise. In the face of such
diversity crises, sequencing many of species of amphibians has enormous to provide
insight into novel antimicrobial compounds, given that many species of frogs harbor a
diverse array of such compounds (NEW REF: in comments). The same peptide
sequence is rarely recovered from closely related species. Genomic approaches to
searching for such antimicrobial diversity using stem cell lines, transcriptomes, and
whole genomic sequencing, is clearly warranted.
Fishes
Fishes include all non-tetrapod vertebrates comprising (i) jawless vertebrates
(hagfishes and lampreys, 108 species), (ii) chondrichthyans (sharks, rays, chimeras,
970 species), (iii) actinopterygians (ray-fin fishes, 26,950 species), and (iv) piscine
sarcopterygians (coelacanths, lungfishes, 8 species). Total described diversity
comprises approximately 28,036 species [31], but actual diversity is probably greater
than 50,000 species. A broad outline of the evolution of these most deeply coalescing of
the vertebrate clades is provided by Stiassny et al. (2004) [32].
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In keeping with their very ancient origins, fishes account for nearly 50% of all
living species of vertebrates, exhibiting a vast diversity in their morphology, physiology,
behavior and ecological adaptations, and providing an exceptional opportunity to study
basic vertebrate biology.
Fishes are also a commercially important group of vertebrates as a food crop
totaling about US $51 billion in trade per year, increasingly driven by the aquaculture
industry [33]. Some 16% of all protein consumed is fish protein, and about one billion
people depend on fishes as their major source of protein. Because of the great demand,
many groups of fishes are over-exploited. Molecular data for commercially important
species of fishes, especially those that are currently endangered and those raised by
aquaculture, will be valuable in designing strategies for maintaining sustainable stocks
and combating disease and other threats.
Fish tissues for the Genome 10K project reside in a number of institutions and
are usually curated as parts of formal institutional collections. The total number of
species represented by tissue samples is not known, but 6,400 species have been
DNA-barcoded and collections of new species continue to be added. Fresh material
from many commonly available species can be obtained easily from fishing boats and
the pet-trade industry for both genome and other molecular projects. The Genome 10K
project has in hand suitable samples from 60/62 orders (97%), 382/492 families (78%),
1,270 of about 3,006 genera (42%) and 2,667 of about 11,430 species (23%),
(Appendix 2, fish).
The largest known animal genome is that of the marbled lungfish, Protopterus
aethiopicus, with a haploid size of 133 pg (about 130Gb), followed by the salamanders
Necturus lewisi and Necturus punctatus at 120pg (about 117Gb) [10]. The genomes are
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bloated through the activity of transposons which, combined with their enormous size,
make genome sequencing and assembly extremely challenging. While RNAsequencing is one avenue by which we may get direct access to interesting biology in
these species, we recommend that full genome sequencing projects for selected largegenome species be undertaken nonetheless. There are important questions pertaining
to gene regulation, genome structure and genome evolution that cannot be answered
from analysis of transcribed RNA alone.
Discussion
Careful observations of the morphological and functional adaptations in
vertebrates have formed the basis of biological studies for a millennium, but it is only
very recently that we are able to observe the action of evolution directly at the genetic
level. It is not known whether convergent adaptations in independent lineages are often
governed by analogous changes in a small number of orthologous genome loci or if
macro-evolutionary events in separate lineages usually result from entirely idiosyncratic
combinations of mutations. Evidence from several recent studies point toward the
former hypothesis (still need to get the best cites). For example, adaptive hind limb
reduction occurred independently many times in different lineages and even within the
same species, just as sticklebacks in different lakes adapted from an ocean to a
freshwater environment [34]. These stickleback adaptations are all traced to
independent deletions of the same distal enhancer of the PITX2 development gene,
demonstrating remarkable convergent evolution at the genomic level [35]. By cataloging
the footprints of adaptive evolution in every genomic locus on every vertebrate lineage,
the Genome 10K project will provide the power to thoroughly test the “same adaptation,
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same loci” hypothesis, along with other fundamental questions about molecular
adaptive mechanisms.
In the course of this investigation, we will discover the genetic loci governing
fundamental vertebrate processes. The study of the evolution of viviparity is an
outstanding example. Birds, crocodiles and turtles all lay eggs, while apart from
monotremes, mammals are all live-bearers. Thus, we found one fundamental transition
from oviparity to viviparity in these amniotes, which caused a fundamental
reorganization in the developmental program and large-scale change in gene
interactions that we are only just beginning to understand.
Remarkably however, non-avian reptiles have an estimated 108 independent
evolution origins of viviparity. Fish have an equally spectacular variety of such
transitions, along with some amphibians, such as the frog genus Gastrotheca, which
includes species with placental-like structures. These many independent instances of
the evolution of viviparity afford an extraordinary opportunity to explore the genomics
behind this reproductive strategy.
The architecture of sex determination in vertebrates is similarly diverse, with
examples of XY, ZW and temperature dependent mechanisms. This provides an equally
exciting opportunity. In fact, a few vertebrate species have abandoned sex altogether.
What happens when an asexual genome descends from an ancestral sexual genome,
as has occurred repeatedly in Aspidoscelis lizard lineages? Are the independent
parthenogenetic genomes parallel in any way? In one group of lizards, genus
Darevskia, the formation of unisexual species is phylogenetically constrained, yet in
others, e.g., Aspidoscelis, it is not. Many species of lizards and snakes are also known
to have facultative parthenogenesis: unmated females produce viable eggs and
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offspring. Unisexuality also occurs in amphibians and fishes by gynogenesis,
hybridogenesis, and in amphibians by kleptogenesis [citation in COMMENT]. Sequential
hermaphrodite fishes can change their sex. Do these parallel convergent changes
involve the same genes? By identifying the genomic loci that support different
evolutionary innovations, such analyses will drive fundamental progress in molecular
and developmental biology, as have discoveries of the molecular basis for human
diseases.
The diversity of vertebrate species that cohabit on our planet attests to
underlying life processes with remarkable potential. Genomics reveals a unity behind
these life processes that is unrivaled by any other avenue of investigation, exposing an
undeniable molecular relatedness and common origin among species. By revealing
genetic vulnerabilities in endangered species and tracking host-pathogen interactions
and coevolution, genomics plays an increasing role in sustaining biodiversity and
tracking emerging infectious diseases. Access to the information contained in the
genomes of threatened and endangered species is an important component of the
Genome 10K project and provides crucial information for comparative vertebrate
genomics, while generating information that may assist conservation efforts [36] [37]. In
studying the genomes of recently extinct species as well, molecular aspects of species
vulnerability are revealed and vital gaps in the vertebrate record restored. In all these
ways, the Genome 10K project will engage the public in the quest for the scientific basis
of animal diversity and in the application of the knowledge we gain to improve animal
health and species conservation.
As Guttenberg altered the course of human history with the publication of the first
book, so did the human genome project forever change the course of the life sciences
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with the publication of the first full vertebrate genome sequence. When Guttenberg’s
success was followed by the publication of other books, libraries naturally emerged to
hold the fruits of this new technology for the benefit of all who sought to imbibe the vast
knowledge made available by the new print medium. We must now follow the human
genome project with a library of vertebrate genomes, a genomic ark for thriving and
threatened species alike, and a permanent digital recording of countless molecular
triumphs and stumbles across some 500 million years of evolutionary episodes that
forged the “endless forms most beautiful” that make up our living world.
Methods:
Branch length estimates:
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Appendix 1: Policy issues

The Genome 10K consortium members recognize this endeavor to be a
noncommercial research program without “reach-through” intellectual property (IP)
agreements.

All individual(s)/institute(s) contributing biomaterials for sequencing thus comply
with the above mentioned noncommercial policy and acknowledge that contributed
samples have been collected and distributed in accordance with applicable national and
international laws and regulations.

The reference materials used for genome sequencing should be clearly
identified, accessible and where possible, adhere to best practices for biodiversity
repositories (particularly concerning taxonomic identification of voucher
specimens/tissues and genome size estimation [38]). Reference documentation should
include digital images/CT scans of the morphological voucher specimens, geospatial
coordinates of the specimen collection site [39] and other emerging metadata standards
proposed for genome sequences [40].

Deposition and publication will follow the Ft Lauderdale agreement in accord with
prior best practices in genomic research, including release of primary sequence data to
the international databases within 24 hours and release of the full genome assemblies
as soon as quality assurance is complete.

Consortium is committed to building programs for training of highly qualified
personnel, particularly in developing nations.
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Appendix 2: Detailed table of classes, orders, families, genera and species
Group
Orders
Families
Genera
Species
Mammals
Afrosoricida
2/2 - 100%
7/19 - 36%
7/51 - 13%
Mammals
Artiodactyla
10/10 - 100%
81/89 - 91%
156/240 - 65%
Mammals
Carnivora
15/15 - 100%
82/126 - 65%
131/287 - 45%
Mammals
Cetacea
11/11 - 100%
38/40 - 95%
80/84 - 95%
Mammals
Chiroptera
13/18 - 72%
74/203 - 36%
162/1116 - 14%
Mammals
Cingulata
1/1 - 100%
3/9 - 33%
4/21 - 19%
Mammals
Dasyuromorphia
2/3 - 66%
3/23 - 13%
3/71 - 4%
Mammals
Dermoptera
1/1 - 100%
1/2 - 50%
1/2 - 50%
Mammals
Didelphimorphia
1/1 - 100%
6/17 - 35%
8/87 - 9%
Mammals
Diprotodontia
11/11 - 100%
19/39 - 48%
27/143 - 18%
Mammals
Erinaceomorpha
1/1 - 100%
4/10 - 40%
6/24 - 25%
Mammals
Hyracoidea
1/1 - 100%
3/3 - 100%
4/4 - 100%
Mammals
Lagomorpha
2/3 - 66%
7/13 - 53%
16/92 - 17%
Mammals
Macroscelidea
1/1 - 100%
3/4 - 75%
3/15 - 20%
Mammals
Microbiotheria
1/1 - 100%
1/1 - 100%
1/1 - 100%
Mammals
Monotremata
2/2 - 100%
2/3 - 66%
2/5 - 40%
Mammals
Notoryctemorphia
1/1 - 100%
1/1 - 100%
1/2 - 50%
Mammals
Paucituberculata
1/1 - 100%
3/3 - 100%
3/6 - 50%
Mammals
Peramelemorphia
2/3 - 66%
3/8 - 37%
3/21 - 14%
Mammals
Perissodactyla
3/3 - 100%
6/6 - 100%
16/17 - 94%
Mammals
Pholidota
1/1 - 100%
1/1 - 100%
6/8 - 75%
Mammals
Pilosa
4/4 - 100%
5/5 - 100%
7/10 - 70%
Mammals
Primates
14/15 - 93%
54/69 - 78%
145/376 - 38%
Mammals
Proboscidea
1/1 - 100%
2/2 - 100%
3/3 - 100%
Mammals
Rodentia
29/33 - 87%
118/481 - 24%
274/2277 - 12%
Mammals
Scandentia
2/2 - 100%
3/5 - 60%
9/20 - 45%
Mammals
Sirenia
2/2 - 100%
2/3 - 66%
2/5 - 40%
Mammals
Soricomorpha
3/4 - 75%
19/45 - 42%
26/428 - 6%
Mammals
Tubulidentata
1/1 - 100%
1/1 - 100%
1/1 - 100%
Birds
Anseriformes
3/3 - 100%
41/52 - 78%
129/162 - 79%
Birds
Apodiformes
2/3 - 66%
97/125 - 77%
238/429 - 55%
Birds
Caprimulgiformes
5/5 - 100%
17/22 - 77%
47/118 - 39%
Birds
Charadriiformes
14/18 - 77%
66/90 - 73%
208/383 - 54%
Page 20
Group
Orders
Families
Genera
Species
Birds
Ciconiiformes
3/3 - 100%
32/39 - 82%
69/116 - 59%
Birds
Coliiformes
1/1 - 100%
2/2 - 100%
5/6 - 83%
Birds
Columbiformes
1/2 - 50%
31/44 - 70%
129/311 - 41%
Birds
Coraciiformes
9/11 - 81%
34/51 - 66%
96/209 - 45%
Birds
Cuculiformes
1/1 - 100%
22/36 - 61%
53/138 - 38%
Birds
Falconiformes
3/3 - 100%
60/83 - 72%
145/304 - 47%
Birds
Galliformes
5/5 - 100%
56/80 - 70%
131/290 - 45%
Birds
Gaviiformes
1/1 - 100%
1/1 - 100%
3/5 - 60%
Birds
Gruiformes
9/10 - 90%
32/59 - 54%
73/196 - 37%
Birds
Musophagiformes
1/1 - 100%
5/6 - 83%
16/23 - 69%
Birds
Opisthicomiformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Birds
Passeriformes
90/107 - 84%
838/1226 - 68%
2796/5756 - 48%
Birds
Pelecaniformes
7/7 - 100%
8/9 - 88%
30/62 - 48%
Birds
Phaethontiformes
1/1 - 100%
1/1 - 100%
3/3 - 100%
Birds
Phoenicopteriformes
1/1 - 100%
3/3 - 100%
4/5 - 80%
Birds
Piciformes
5/5 - 100%
53/68 - 77%
255/398 - 64%
Birds
Podicipediformes
1/1 - 100%
5/6 - 83%
11/22 - 50%
Birds
Procellariiformes
4/4 - 100%
19/27 - 70%
52/112 - 46%
Birds
Psittaciformes
1/1 - 100%
67/85 - 78%
186/364 - 51%
Birds
Sphenisciformes
1/1 - 100%
6/6 - 100%
13/17 - 76%
Birds
Strigiformes
2/2 - 100%
21/29 - 72%
64/195 - 32%
Birds
Struthioniformes
6/6 - 100%
14/15 - 93%
37/59 - 62%
Birds
Trogoniformes
1/1 - 100%
5/6 - 83%
25/39 - 64%
Amphibians
Anura
32/48 - 66%
107/411 - 26%
302/5532 - 5%
Amphibians
Caudata
10/10 - 100%
32/66 - 48%
86/552 - 15%
Amphibians
Gymnophiona
3/3 - 100%
5/33 - 15%
6/176 - 3%
Reptiles
Testudines
10/14 - 71%
43/98 - 43%
60/295 20%
Reptiles
Sphenodontia
1/1 - 100%
1/1 - 100%
1/1 100%
Reptiles
Squamata
35/41 - 85%
309/758 - 40%
735/3996 18%
Reptiles
Crocodylia
1/1 - 100%
8/9 - 89%
21/25 - 84%
Fishes
Petromyzontiformes
1/1 - 100%
2/10 - 20%
2/38 - 5%
Fishes
Myxiniformes
1/1 - 100%
2/6 - 33%
3/24 - 12%
Fishes
Rajiformes
1/1 - 100%
8/16 - 50%
25/107 - 23%
Fishes
Torpediniformes
2/4 - 50%
2/5 - 40%
5/15 - 33%
Fishes
Heterodontiformes
1/1 - 100%
1/1 - 100%
3/5 - 60%
Page 21
Group
Orders
Families
Genera
Species
Fishes
Squaliformes
1/1 - 100%
2/2 - 100%
14/19 - 73%
Fishes
Orectolobiformes
5/5 - 100%
7/8 - 87%
13/17 - 76%
Fishes
Carcharhiniformes
6/8 - 75%
27/37 - 72%
70/140 - 50%
Fishes
Echinorhiniformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Fishes
Lamniformes
5/5 - 100%
8/10 - 80%
11/14 - 78%
Fishes
Hexanchiformes
3/3 - 100%
4/4 - 100%
5/6 - 83%
Fishes
Chimaeriformes
3/3 - 100%
4/4 - 100%
9/18 - 50%
Fishes
Lepidosireniformes
2/2 - 100%
2/2 - 100%
2/8 - 25%
Fishes
Ceratodontiformes
0/1 - 0%
0/1 - 0%
0/1 - 0%
Fishes
Coelacanthiformes
1/1 - 100%
1/1 - 100%
1/2 - 50%
Fishes
Acipenseriformes
2/2 - 100%
3/7 - 42%
5/38 - 13%
Fishes
Semionotiformes
1/1 - 100%
2/2 - 100%
4/7 - 57%
Fishes
Amiiformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Fishes
Elopiformes
2/2 - 100%
2/2 - 100%
5/7 - 71%
Fishes
Anguilliformes
14/15 - 93%
27/70 - 38%
52/159 - 32%
Fishes
Clupeiformes
4/6 - 66%
20/53 - 37%
38/142 - 26%
Fishes
Cypriniformes
4/5 - 80%
43/327 - 13%
92/1588 - 5%
Fishes
Characiformes
10/13 - 76%
44/104 - 42%
78/325 - 24%
Fishes
Siluriformes
14/37 - 37%
45/282 - 15%
71/929 - 7%
Fishes
Gymnotiformes
4/7 - 57%
5/21 - 23%
5/45 - 11%
Fishes
Esociformes
2/2 - 100%
4/4 - 100%
7/11 - 63%
Fishes
Salmoniformes
4/4 - 100%
17/36 - 47%
27/188 - 14%
Fishes
Gadiformes
9/11 - 81%
31/52 - 59%
54/132 - 40%
Fishes
Batrachoidiformes
1/1 - 100%
4/9 - 44%
7/16 - 43%
Fishes
Lophiiformes
10/12 - 83%
16/24 - 66%
21/45 - 46%
Fishes
Cyprinodontiformes
8/9 - 88%
29/109 - 26%
87/626 - 13%
Fishes
Beloniformes
5/5 - 100%
17/31 - 54%
36/97 - 37%
Fishes
Scorpaeniformes
20/32 - 62%
63/130 - 48%
149/465 - 32%
Fishes
Perciformes
114/151 - 75%
492/1108 - 44%
1213/4698 - 25%
Fishes
Pleuronectiformes
11/11 - 100%
64/95 - 67%
91/213 - 42%
Fishes
Osteoglossiformes
6/6 - 100%
9/28 - 32%
10/142 - 7%
Fishes
Polypteriformes
0/1 - 0%
0/2 - 0%
0/9 - 0%
Fishes
Gonorynchiformes
2/4 - 50%
2/7 - 28%
2/10 - 20%
Fishes
Mugiliformes
1/1 - 100%
5/8 - 62%
6/26 - 23%
Fishes
Tetraodontiformes
10/10 - 100%
51/69 - 73%
92/181 - 50%
Page 22
Group
Orders
Families
Genera
Species
Fishes
Myliobatiformes
6/7 - 85%
18/22 - 81%
57/112 - 50%
Fishes
Atheriniformes
6/8 - 75%
13/33 - 39%
19/174 - 10%
Fishes
Synbranchiformes
2/2 - 100%
5/6 - 83%
6/19 - 31%
Fishes
Beryciformes
7/7 - 100%
12/18 - 66%
30/49 - 61%
Fishes
Stomiiformes
6/7 - 85%
18/21 - 85%
30/52 - 57%
Fishes
Albuliformes
1/1 - 100%
1/2 - 50%
2/14 - 14%
Fishes
Pristiformes
1/1 - 100%
2/2 - 100%
4/5 - 80%
Fishes
Zeiformes
4/5 - 80%
8/11 - 72%
12/17 - 70%
Fishes
Gasterosteiformes
7/10 - 70%
21/37 - 56%
31/98 - 31%
Fishes
Myctophiformes
2/2 - 100%
18/32 - 56%
28/90 - 31%
Fishes
Aulopiformes
12/14 - 85%
24/32 - 75%
36/68 - 52%
Fishes
Lampridiformes
6/6 - 100%
8/9 - 88%
10/15 - 66%
Fishes
Percopsiformes
2/3 - 66%
2/3 - 66%
2/4 - 50%
Fishes
Polymixiiformes
1/1 - 100%
1/1 - 100%
3/4 - 75%
Fishes
Stephanoberyciformes
5/7 - 71%
9/17 - 52%
10/49 - 20%
Fishes
Dactylopteriformes
1/1 - 100%
2/2 - 100%
3/4 - 75%
Fishes
Ophidiiformes
3/3 - 100%
12/18 - 66%
14/24 - 58%
Fishes
Argentiniformes
4/6 - 66%
8/21 - 38%
13/32 - 40%
Fishes
Ateleopodiformes
1/1 - 100%
1/2 - 50%
1/3 - 33%
Fishes
Notacanthiformes
2/2 - 100%
4/4 - 100%
6/7 - 85%
Fishes
Rhiniformes
1/1 - 100%
1/1 - 100%
1/1 - 100%
Fishes
????
9/10 - 90%
15/24 - 62%
32/74 - 43%
Page 23
Appendix 3: Technological issues
(To be provided)
Page 24
Authors:
Coordinators: David Haussler, Stephen J. O’Brien, Oliver Ryder
Mammals Group Members: Scott Baker, James Estes, Jennifer Graves, Alexander
Graphodatsky, Kris Helgen, *Warren Johnson, Harris Lewin, Gordon Luikart, *William
Murphy, Steve O’Brien, Oliver Ryder, Mark Springer, Emma Teeling, Terrie Williams,
Nathan Wolfe, YaPing Zhang
Birds Group Members: *Keith Barker, Joel Cracraft, Scott Edwards, Olivier Hanotte,
*Fred Sheldon
Amphibians and Reptiles Group Members: *Andrew J. Crawford, Matthew LeBreton,
Paolo Martelli, *Jim McGuire, *Robert Murphy, Brad Shaffer, *Barry Sinervo
Fishes Group Members: Fred Allendorf, Giacomo Bernardi, Guillamo Orti, David
Rawson, *Byrappa Venkatesh, Robert Vrijenhoek, Robert Ward, *Ed Wiley
General Policy Group Members: Scott Baker, *Adam Felsenfeld, Eric Green, *Robert
Hanner, *Olivier Hanotte, David Haussler, Paul Hebert, Steve O'Brien, Oliver Ryder,
Hector Seuanez, YaPing Zhang
Analysis Group Members: *Michele Clamp, Mark Diekhans, David Haussler, Bailey
Kessing, David Kingsley, *Webb Miller, Ngan Nguyen, Brian Pike, Stephan Schuster,
Josh Stuart, Steve Turner
*Chairs
Page 25
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Lander, E.S., et al., Initial sequencing and analysis of the human genome.
Nature, 2001. 409(6822): p. 860-921.
3.
Venter, J.C., et al., The sequence of the human genome. Science, 2001.
291(5507): p. 1304-51.
4.
Sodergren, E., et al., The genome of the sea urchin Strongylocentrotus
purpuratus. Science, 2006. 314(5801): p. 941-52.
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Dehal, P., et al., The draft genome of Ciona intestinalis: insights into chordate
and vertebrate origins. Science, 2002. 298(5601): p. 2157-67.
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Holland, L.Z., et al., The Amphioxus genome illuminates vertebrate origins and
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Hillier, L.W., et al., Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution. Nature, 2004. 432(7018): p.
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Aparicio, S., et al., Whole-genome shotgun assembly and analysis of the
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Osorio, J. and S. Retaux, The lamprey in evolutionary studies. Dev Genes Evol,
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Baker, C.V., The evolution and elaboration of vertebrate neural crest cells. Curr
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Meulemans, D. and M. Bronner-Fraser, Amphioxus and lamprey AP-2 genes:
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Waterston, R.H., et al., Initial sequencing and comparative analysis of the mouse
genome. Nature, 2002. 420(6915): p. 520-62.
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Siepel, A., et al., Evolutionarily conserved elements in vertebrate, insect, worm,
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King, M.C. and A.C. Wilson, Evolution at two levels in humans and chimpanzees.
Science, 1975. 188(4184): p. 107-16.
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Bejerano, G., et al., Ultraconserved elements in the human genome. Science,
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18.
Edwards, S., S. Birks, and R. Brumfield, Future of avian genetic resources
collections: Archives of evolutionary and environmental history. Auk, 2005(122):
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Brumfield, R., Pers. Comm. 2009: Louisianna State University.
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Seutin, G., B. White, and P. Boag, Preservation of avian blood and tissue
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Okita, K., T. Ichisaka, and S. Yamanaka, Generation of germline-competent
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Stadtfeld, M., et al., Induced pluripotent stem cells generated without viral
integration. Science, 2008. 322(5903): p. 945-9.
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Yu, J., et al., Human induced pluripotent stem cells free of vector and transgene
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Townsend, T., et al., Molecular phylogenetics of Squamata: the position of
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Roelants, K., et al., Global patterns of diversification in the history of modern
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Tidwell, J.H. and G.L. Allan, Fish as food: aquaculture's contribution. Ecological
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Shapiro, M.D., M.A. Bell, and D.M. Kingsley, Parallel genetic origins of pelvic
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Kingsley, D., pers comm, Genome10K, Editor. 2009: Santa Cruz.
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Ryder, O.A., et al., DNA banks for endangered animal species. Science, 2000.
288(5464): p. 275-7.
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Ryder, O.A., Conservation genomics: applying whole genome studies to species
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Hanner, R.H. and T.R. Gregory, Genomic diversity research and the role of
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Field, D., Working together to put molecules on the map. Nature, 2008.
453(7198): p. 978.
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Field, D., et al., The minimum information about a genome sequence (MIGS)
specification. Nature Biotechnology, 2008. 26(5): p. 541-547.
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Frost, D.R., Amphibian Species of the World: an Online Reference., in Version
5.3 (12 February, 2009). 2009, American Museum of Natural History, New York,
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42.
Wilson, D.E. and D.M. Reeder, Mammal species of the world : a taxonomic and
geographic reference. 3rd ed. 2005, Baltimore: Johns Hopkins University Press.
2 v. (xxxv, 2142 p.).
43.
Howard, R., A. Moore, and E.C. Dickinson, The Howard and Moore complete
checklist of the birds of the world. Rev. and enl. 3rd ed. 2003, Princeton, N.J.:
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Page 28
Please chairs proof these numbers; they are the meat of the White paper
Add column for coalescence date time for each group also chairs??
The time to most recent common ancestor of amphibians (extant Lissamphibia) dates to 260 Ma
(REF: Marjanović, D. and M. Laurin, Fossils, molecules, divergence times, and the origin of
lissamphibians. Systematic Biology, 2007. 56: p. 369-388.
I’ve been sending all our tissue and species lists to the G10K database so I imagine that Mark and
Ngan could get these numbers at the click of a button, yes?
Table 1: Vertebrate taxa [41]
Group
Orders
Families
Genera
Species
Mammals
29/29
100%
139/153 91%
552/1231
45%
1107/5417
20%
Birds
27/27
100%
179/205 87%
1537/2172
71%
4819/9723
50%
Amphibians
3/3
100%
45/61
74%
144/510
28%
394/ 6,529
6%
Reptiles
4/4
100%
47/69
67%
361/1066
34%
817/8442
10%
60/62
97%
382/515 74%
1270/4494
28%
2667/27977
10%
Fishes
Extant of the current Genome 10K collection is tabulated as (number of species in collection) / (total
number of species) and percentage with similar summaries for genera, families and orders. The total
numbers are computed using the NCBI taxonomy (www. ncbi.nlm.nih.gov), but substituted the Wilson
and Reeder [42] tree for the mammals and the Howard and Moore [43] tree for birds. Amphibian
taxonomy follows Frost [41] with modifications by Roelants et al. [NEW REF in comments SEE ALSO
FIGURE 5, 2007] and total number of species taken from AmphibiaWeb [44].
Page 29
Table 2: List of collections and participating institutions (Fill this in)
Institutions
Steward(s)
Academy of Natural Sciences, Philadelphia
NEED TABLE OF SAMPLES
Web address
http://research.amnh.org/ornithology/personnel/jlc.h
tm
American Museum of Natural History
Joel Cracraft
Australian National University
NEED TABLE OF SAMPLES
Biodiversity Research Institute, University of Kansas
Edward Wiley
Burke Museum, University of Washington
NEED TABLE OF SAMPLES
Círculo Herpetológico de Panamá
Roberto Ibáñez
CSIRO Marine and Atmospheric Research
Robert Ward
http://www.cmar.csiro.au/anfc/
CTR for Reproduction of Endangered Species-San Diego
Zoo
Oliver Ryder
http://www.sandiegozoo.org/conservation/about/ad
ministrators/oliver_ryder_ph.d/
Departamento de Zoologia, I.B., UNESP, Sao Paulo
Célio F. B. Haddad
http://ns.rc.unesp.br/ib/zoologia/anuros/index.html
Ocean Park Corporation, Hong Kong
Paolo Martelli
www.oceanpark.com.hk
Institute of Cytology and Genetics, Russian Academy,
Siberian Branch
Alexander Graphodatsky
http://www.bionet.nsc.ru/indexEngl.html
Institute of Molecular and Cell Biology, Singapore
NEED TABLE OF SAMPLES
Kunming Institute of Zoology, Chinese Academy of Sciences
NEED TABLE OF SAMPLES
LIRANS Institute, University of Bedfordshire, UK,
David Rawson
Louisiana State University Museum of Zoology
NEED TABLE OF SAMPLES
http://www.nhm.ku.edu/fishes/
http://www.beds.ac.uk/research/lirans/personnel/ra
wson_d
Page 30
Institutions
Steward(s)
Web address
LSU Museum of Natural Science
Fred Sheldon
http://appl003.lsu.edu/natsci/lmns.nsf/$Content/Sh
eldon?OpenDocument
Marine Mammal Institute, Oregon State University
Scott Baker
http://mmi.oregonstate.edu/
Monterey Bay Aquarium Research Institute
NEED TABLE OF SAMPLES
Museo Nacional de Ciencias Naturales (MNCN), Madrid
David R. Vieites
http://www.vieiteslab.com
Museu de Zoologia da Universidade de São Paulo
Hussam Zaher
http://www.mz.usp.br/
Museum of Comparative Zoology, Harvard*
NEED TABLE OF SAMPLES
Museum of Vertebrate Zoology (MVZ)
NEED TABLE OF SAMPLES
Museum of Vertebrate Zoology, UC Berkeley
NEED TABLE OF SAMPLES
Museum Victoria, Australia
NEED TABLE OF SAMPLES
National Cancer Institute Lab of Genomic Diversity
Stephen O’Brien
Natural History Museum of Los Angeles County
NEED TABLE OF SAMPLES
Royal Ontario Museum (ROM)
Robert Murphy
http://labs.eeb.utoronto.ca/murphy/
Smithsonian Institution, National Museum of Natural History
Roy W. McDiarmid
http://vertebrates.si.edu/herps/
Smithsonian Tropical Research Institute
Eldredge Bermingham
http://www.stri.org/
South Australian Museum
Steve Donnellan
http://www.samuseum.sa.gov.au/page/default.asp?
site=1&id=1307
Swedish Museum of Natural History
NEED TABLE OF SAMPLES
Texas A&M University
William Murphy
http://gene.tamu.edu/faculty_pages/faculty_Murphy
W.php
Field Museum of Natural History, Chicago
Harold K. Voris
http://www.fieldmuseum.org/research_collections/z
http://home.ncifcrf.gov/ccr/lgd/
Page 31
Institutions
Steward(s)
Web address
oology/
Universidade Estadual Paulista (Departamento de Zoologia,
Instituto de Biociências), Rio Claro, Brasil
Célio F. B. Haddad
http://www.rc.unesp.br/ib/zoologia/
UCLA, Institute of the Environment
Matthew LeBreton
http://www.ioe.ucla.edu/ctr/staff/LeBreton_Matthew
.html
University College-Dublin
NEED TABLE OF SAMPLES
University of California, Riverside
NEED TABLE OF SAMPLES
University of California, Santa Cruz
NEED TABLE OF SAMPLES
University of Montana
NEED TABLE OF SAMPLES
University of Nebraska, Lincoln
Guillermo Orti
University of Nevada, Las Vegas
NEED TABLE OF SAMPLES
University of Texas at Arlington
Jonathan A. Campbell
http://biology.uta.edu/herpetology/
Zoological Institute, Technical University of
Braunschweig
Miguel Vences
http://www.mvences.de/
Zoological Museum of Copenhagen, Denmark
NEED TABLE OF SAMPLES
http://golab.unl.edu/index.html
Page 32
Figure legends (need these) (Fill in references)
Legend(s) here
Page 33
Figure 1: A phylogenetic view of the vertebrate subclass
Page 34
Figure 2: The mammalian radiations
Page 35
Figure 3: The birds of the world
Page 36
Figure 4: The reptiles of today (Two NEW REFS: in comments)
Page 37
Figure 5: The amphibians’ phylogeny (NEW REF: Roelants et al. 2007)
Page 38