Table S4. Candidate speciation genes identified from genome-wide scans for positive selection.

GO term / Descriptions / Basalt only / Chalk only / Both / Isolation
GO:0035270 / endocrine system development / Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands, which include the ovaries and testes. / Pde3b, Cga / Pbx1 / postmating
GO:0060065 / uterus development / The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure. / Esr1, Rbp4 / postmating
GO:0060068 / vagina development / The reproductive developmental process whose specific outcome is the progression of the vagina over time, from its formation to the mature structure. / Esr1, Rbp4 / postmating
GO:0048806 / genitalia development / The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure. / Pdgfra, Rbp4 / postmating
GO:0035112 / genitalia morphogenesis / The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal. / Rbp4 / postmating
GO:0046545 / development of primary female sexual characteristics / The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion. / Esr1, Rbp4 / postmating
GO:0046660 / female sex differentiation / The establishment of the sex of a female organism by physical differentiation. / Esr1, Rbp4 / postmating
GO:0001541 / ovarian follicle development / The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure. / Esr1 / postmating
GO:0032275 / luteinizing hormone secretion / The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. / Cga / postmating
GO:0030540 / female genitalia development / The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure. / Rbp4 / postmating
GO:0048807 / female genitalia morphogenesis / The process in which the anatomical structures of female genitalia are generated and organized. / Rbp4 / postmating
GO:0042698 / ovulation cycle / The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. / Esr1 / postmating
GO:0001547 / antral ovarian follicle growth / Increase in size of antral follicles due to cell proliferation and/or growth of the antral cavity. / Esr1 / postmating
GO:0007565 / female pregnancy / The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. / Esr1 / postmating
GO:0060135 / maternal process involved in female pregnancy / A reproductive process occurring in the mother that allows an embryo or fetus to develop within it. / Esr1 / postmating
GO:0008585 / female gonad development / The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. / Esr1 / postmating
GO:0030284 / estrogen receptor activity / Combining with estrogen and transmitting the signal within the cell to trigger a change in cell activity or function. / Esr1 / postmating
GO:0030879 / mammary gland development / The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages. / Esr1 / postmating
GO:0022602 / ovulation cycle process / A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years. / Esr1 / postmating
GO:0003006 / reproductive developmental process / A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. / Esr1, Ppp2r2b, Pdgfra, Rbp4, Cga, Mei1 / Piwil1, Pbx1 / postmating
GO:0007548 / sex differentiation / The establishment of the sex of an organism by physical differentiation. / Esr1, Pdgfra, Rbp4, Cga / Pbx1 / postmating
GO:0048610 / reproductive cellular process / OBSOLETE. A process, occurring at the cellular level that is involved in the reproductive function of a multicellular or single-celled organism. / Ppp2r2b, Rbp4, Mei1 / Piwil1 / postmating
GO:0045137 / development of primary sexual characteristics / The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. / Esr1, Pdgfra, Rbp4, Cga / postmating
GO:0048609 / reproductive process in a multicellular organism / The process, occurring above the cellular level that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. / Esr1, Ppp2r2b, Rbp4, Mei1 / Piwil1, Cit / Htt / postmating
GO:0007276 / gamete generation / The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. / Ppp2r2b, Rbp4, Mei1 / Piwil1, Cit / Htt / postmating
GO:0048608 / reproductive structure development / The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures. / Esr1, Rbp4, Cga / postmating
GO:0051321 / meiotic cell cycle / Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. / Mei1 / Piwil1, Meig1 / postmating
GO:0019953 / sexual reproduction / A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) joins up so that homologous sequences are aligned with each other, and this is followed by the exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. / Ppp2r2b, Rbp4, Mei1 / Piwil1, Cit / Htt / postmating
GO:0032504 / multicellular organism reproduction / The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. / Esr1, Ppp2r2b, Rbp4, Mei1 / Piwil1, Cit / Htt / postmating
GO:0046546 / development of primary male sexual characteristics / The process whose specific outcome is the progression of the primary male sexual characteristics over time, from their formation to the mature structures. The primary male sexual characteristics are the testes, and they develop in response to sex hormone secretion. / Esr1, Pdgfra, Rbp4 / postmating
GO:0007281 / germ cell development / The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. / Ppp2r2b, Rbp4, Mei1 / Piwil1 / postmating
GO:0046661 / male sex differentiation / The establishment of the sex of a male organism by physical differentiation. / Esr1, Pdgfra, Rbp4 / postmating
GO:0007286 / spermatid development / The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. / Ppp2r2b, Mei1 / Piwil1 / postmating
GO:0048515 / spermatid differentiation / The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. / Ppp2r2b, Mei1 / Piwil1 / postmating
GO:0048232 / male gamete generation / Generation of the male gamete; specialized haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction. / Ppp2r2b, Rbp4, Mei1 / Piwil1, Cit / Htt / postmating
GO:0008406 / gonad development / The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. / Esr1, Rbp4, Cga / postmating
GO:0043627 / response to estrogen stimulus / Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics. / Esr1 / Tbl1x / postmating
GO:0008584 / male gonad development / The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure. / Esr1, Rbp4 / postmating
GO:0060527 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / The branching morphogenesis process in which the prostate epithelial cords branch freely to create the structure of the prostate acini. / Esr1 / postmating
GO:0060443 / mammary gland morphogenesis / The process in which anatomical structures of the mammary gland are generated and organized. Morphogenesis refers to the creation of shape. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. / Esr1 / postmating
GO:0060512 / prostate gland morphogenesis / The process in which the anatomical structures of a prostate gland are generated and organized. / Esr1 / postmating
GO:0060737 / prostate gland morphogenetic growth / The differential increase in size or mass of the prostate gland that contributes to the gland attaining its form. / Esr1 / postmating
GO:0032274 / gonadotropin secretion / The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone. / Cga / postmating
GO:0060444 / branching involved in mammary gland duct morphogenesis / The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. / Esr1 / postmating
GO:0046884 / follicle-stimulating hormone secretion / The regulated release of follicle-stimulating hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. / Cga / postmating
GO:0060740 / prostate gland epithelium morphogenesis / The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. / Esr1 / postmating
GO:0060526 / prostate glandular acinus morphogenesis / The process in which the prostate glandular acini are generated and organized. The glandular acini are the saclike structures of the gland. / Esr1 / postmating
GO:0060525 / prostate glandular acinus development / The progression of a glandular acinus of the prostate gland over time, from its initial formation to the mature structure. The glandular acini are the saclike structures of the gland. / Esr1 / postmating
GO:0060523 / prostate epithelial cord elongation / The developmental growth process in which solid chords of prostate epithelium increase in length. / Esr1 / postmating
GO:0033598 / mammary gland epithelial cell proliferation / The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. / Esr1 / postmating
GO:0007140 / male meiosis / A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. / Mei1 / postmating
GO:0060745 / mammary gland branching involved in pregnancy / The process in which the branching structure of the mammary gland duct is generated and organized as a part of pregnancy. / Esr1 / postmating
GO:0008209 / androgen metabolic process / The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics. / Esr1 / postmating
GO:0030850 / prostate gland development / The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. / Esr1 / postmating
GO:0060442 / branching involved in prostate gland morphogenesis / The process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem. / Esr1 / postmating
GO:0060750 / epithelial cell proliferation involved in mammary gland duct elongation / The multiplication or reproduction of mammary gland branch epithelial cells, resulting in the elongation of the branch. The mammary gland branch differs from the bud in that it is not the initial curved portion of the outgrowth. / Esr1 / postmating
GO:0030539 / male genitalia development / The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure. / Pdgfra / postmating
GO:0007284 / spermatogonial cell division / The mitotic divisions of the primary spermatogonial cell (a primordial male germ cell) to form secondary spermatogonia (primary spermatocytes). / Rbp4 / postmating
GO:0060687 / regulation of branching involved in prostate gland morphogenesis / Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem. / Esr1 / postmating
GO:0048136 / male germ-line cyst formation / Formation of a group of interconnected cells derived from a single male gonial founder cell. / Rbp4 / postmating
GO:0007141 / male meiosis I / A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline. / Mei1 / postmating
GO:0060736 / prostate gland growth / The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state. / Esr1 / postmating
GO:0033391 / chromatoid body / A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182). / Piwil1 / postmating
GO:0004984 / olfactory receptor activity / Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell. / Olfr15, Olfr484, Olfr480, Olfr1052 / Premating
GO:0021988 / olfactory lobe development / The progression of the olfactory lobe over time from its initial formation until its mature state. The olfactory lobe is the area of the brain that process the neural inputs for the sense of smell. / Htt / Premating
GO:0007608 / sensory perception of smell / The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. / Olfr15, Olfr484, Olfr480, Olfr1052 / Premating
GO:0021537 / telencephalon development / The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived. / Ncor2 / Htt / Premating